FreeSurfer#
Author: Steffen Bollmann
Citation:
Dataset: MP2RAGE T1-weighted average 7T model (human brain model)
Bollmann, Steffen, Andrew Janke, Lars Marstaller, David Reutens, Kieran O’Brien, and Markus Barth. “MP2RAGE T1-weighted average 7T model” January 1, 2017. doi:10.14264/uql.2017.266
Output CPU information#
!cat /proc/cpuinfo | grep 'vendor' | uniq
!cat /proc/cpuinfo | grep 'model name' | uniq
vendor_id : AuthenticAMD
model name : AMD EPYC 7763 64-Core Processor
# we can use module to load freesurfer in a specific version
import module
await module.load('freesurfer/7.3.2')
await module.list()
['Lmod',
'Warning:',
'The',
'environment',
'MODULEPATH',
'has',
'been',
'changed',
'in',
'unexpected',
'ways.',
'Lmod',
'is',
'unable',
'to',
'use',
'given',
'MODULEPATH.',
'It',
'is',
'using:',
'"/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/functional_imaging:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/rodent_imaging:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/image_registration:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/structural_imaging:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/image_segmentation:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/quantitative_imaging:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/workflows:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/hippocampus:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/image_reconstruction:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/data_organisation:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/electrophysiology:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/phase_processing:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/programming:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/machine_learning:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/diffusion_imaging:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/body:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/visualization:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/spectroscopy:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/quality_control:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/statistics:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/shape_analysis:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/spine:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/molecular_biology:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/bids_apps:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/cryo_EM::".',
'Please',
'use',
'"module',
'use',
'to',
'change',
'MODULEPATH',
'instead.',
'freesurfer/7.3.2']
!recon-all
USAGE: recon-all
Required Arguments:
-subjid <subjid>
-<process directive>
Fully-Automated Directive:
-all : performs all stages of cortical reconstruction
-autorecon-all : same as -all
Manual-Intervention Workflow Directives:
-autorecon1 : process stages 1-5 (see below)
-autorecon2 : process stages 6-23
after autorecon2, check white surfaces:
a. if wm edit was required, then run -autorecon2-wm
b. if control points added, then run -autorecon2-cp
c. proceed to run -autorecon3
-autorecon2-cp : process stages 12-23 (uses -f w/ mri_normalize, -keep w/ mri_seg)
-autorecon2-wm : process stages 15-23
-autorecon2-inflate1 : 6-18
-autorecon2-perhemi : tess, sm1, inf1, q, fix, sm2, inf2, finalsurf, ribbon
-autorecon3 : process stages 24-34
if edits made to correct pial, then run -autorecon-pial
-hemi ?h : just do lh or rh (default is to do both)
Autorecon Processing Stages (see -autorecon# flags above):
1. Motion Correction and Conform
2. NU (Non-Uniform intensity normalization)
3. Talairach transform computation
4. Intensity Normalization 1
5. Skull Strip
6. EM Register (linear volumetric registration)
7. CA Intensity Normalization
8. CA Non-linear Volumetric Registration
9. Remove neck
10. EM Register, with skull
11. CA Label (Aseg: Volumetric Labeling) and Statistics
12. Intensity Normalization 2 (start here for control points)
13. White matter segmentation
14. Edit WM With ASeg
15. Fill (start here for wm edits)
16. Tessellation (begins per-hemisphere operations)
17. Smooth1
18. Inflate1
19. QSphere
20. Automatic Topology Fixer
21. White Surfs (start here for brain edits for pial surf)
22. Smooth2
23. Inflate2
24. Spherical Mapping
25. Spherical Registration
26. Spherical Registration, Contralater hemisphere
27. Map average curvature to subject
28. Cortical Parcellation (Labeling)
29. Cortical Parcellation Statistics
30. Pial Surfs
31. WM/GM Contrast
32. Cortical Ribbon Mask
33. Cortical Parcellation mapped to ASeg
34 Brodmann and exvio EC labels
Step-wise Directives
See -help
Expert Preferences
-pons-crs C R S : col, row, slice of seed point for pons, used in fill
-cc-crs C R S : col, row, slice of seed point for corpus callosum, used in fill
-lh-crs C R S : col, row, slice of seed point for left hemisphere, used in fill
-rh-crs C R S : col, row, slice of seed point for right hemisphere, used in fill
-nofill : do not use the automatic subcort seg to fill
-watershed cmd : control skull stripping/watershed program
-xmask file : custom external brain mask to replace automated skullstripping
-wsless : decrease watershed threshold (leaves less skull, but can strip more brain)
-wsmore : increase watershed threshold (leaves more skull, but can strip less brain)
-wsatlas : use atlas when skull stripping
-no-wsatlas : do not use atlas when skull stripping
-no-wsgcaatlas : do not use GCA atlas when skull stripping
-wsthresh pct : explicity set watershed threshold
-wsseed C R S : identify an index (C, R, S) point in the skull
-norm3diters niters : number of 3d iterations for mri_normalize
-normmaxgrad maxgrad : max grad (-g) for mri_normalize. Default is 1.
-norm1-b N : in the _first_ usage of mri_normalize, use control
point with intensity N below target (default=10.0)
-norm2-b N : in the _second_ usage of mri_normalize, use control
point with intensity N below target (default=10.0)
-norm1-n N : in the _first_ usage of mri_normalize, do N number
of iterations
-norm2-n N : in the _second_ usage of mri_normalize, do N number
of iterations
-cm : conform volumes to the min voxel size
-no-fix-with-ga : do not use genetic algorithm when fixing topology
-fix-diag-only : topology fixer runs until ?h.defect_labels files
are created, then stops
-seg-wlo wlo : set wlo value for mri_segment and mris_make_surfaces
-seg-ghi ghi : set ghi value for mri_segment and mris_make_surfaces
-nothicken : pass '-thicken 0' to mri_segment
-no-ca-align-after : turn off -align-after with mri_ca_register
-no-ca-align : turn off -align with mri_ca_label
-deface : deface subject, written to orig_defaced.mgz
-expert file : read-in expert options file
-xopts-use : use pre-existing expert options file
-xopts-clean : delete pre-existing expert options file
-xopts-overwrite : overwrite pre-existing expert options file
-termscript script : run script before exiting (multiple -termscript flags possible)
This can be good for running custom post-processing after recon-all
The script must be in your path. The subjid is passed as the only argument
The current directory is changed to SUBJECTS_DIR before the script is run
The script should exit with 0 unless there is an error
-mprage : assume scan parameters are MGH MP-RAGE protocol
-washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol.
both mprage flags affect mri_normalize and mri_segment,
and assumes a darker gm.
-schwartzya3t-atlas : for tal reg, use special young adult 3T atlas
-threads num : set number of threads to use
Notification Files (Optional)
-waitfor file : wait for file to appear before beginning
-notify file : create this file after finishing
Status and Log files (Optional)
-log file : default is scripts/recon-all.log
-status file : default is scripts/recon-all-status.log
-noappend : start new log and status files instead of appending
-no-isrunning : do not check whether this subject is currently being processed
Segmentation of substructures of hippocampus and brainstem
(These deprecated; please see segmentHA_T1.sh, segmentHA_T1.sh, segmentHA_T1_long.sh, segmentBS.sh)
-hippocampal-subfields-T1 : segmentation of hippocampal subfields using input T1 scan
-hippocampal-subfields-T2 file ID : segmentation using an additional scan (given by file);
ID is a user-defined identifier for the analysis
-hippocampal-subfields-T1T2 file ID : segmentation using additional scan (given by file) and input T1
simultaneously; ID is a user-defined identifier for the analysis
-brainstem-structures : segmentation of brainstem structures
Other Arguments (Optional)
-sd subjectsdir : specify subjects dir (default env SUBJECTS_DIR)
-mail username : mail user when done
-umask umask : set unix file permission mask (default 002)
-grp groupid : check that current group is alpha groupid
-onlyversions : print version of each binary and exit
-debug : print out lots of info
-allowcoredump : set coredump limit to unlimited
-dontrun : do everything but execute each command
-version : print version of this script and exit
-help : voluminous bits of wisdom
Download data#
![ -f ./mp2rage.nii ] && echo "$FILE exist." || wget https://imaging.org.au/uploads/Human7T/mp2rageModel_L13_work03-plus-hippocampus-7T-sym-norm-mincanon_v0.8.nii -O ./mp2rage.nii
--2025-06-12 21:03:23-- https://imaging.org.au/uploads/Human7T/mp2rageModel_L13_work03-plus-hippocampus-7T-sym-norm-mincanon_v0.8.nii
Resolving imaging.org.au (imaging.org.au)...
203.101.229.7
Connecting to imaging.org.au (imaging.org.au)|203.101.229.7|:443...
connected.
HTTP request sent, awaiting response...
200 OK
Length: 1536000352 (1.4G) [application/octet-stream]
Saving to: ‘./mp2rage.nii’
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./mp2rage.nii 100%[===================>] 1.43G 14.5MB/s in 1m 40s
2025-06-12 21:05:04 (14.6 MB/s) - ‘./mp2rage.nii’ saved [1536000352/1536000352]
!ls
mp2rage.nii
Run#
!mkdir ./freesurfer_output
!recon-all -subject subjectname -i mp2rage.nii -all -sd ./freesurfer_output
fs-check-version --s subjectname --o /tmp/tmp.EVrNnA
Thu Jun 12 21:05:12 UTC 2025
setenv SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
cd /tmp/tmps594ishs
/opt/freesurfer-7.3.2/bin/fs-check-version --s subjectname --o /tmp/tmp.EVrNnA
-rwxrwxr-x 1 121 129 18565 Aug 4 2022 /opt/freesurfer-7.3.2/bin/fs-check-version
freesurfer-linux-centos8_x86_64-7.3.2-20220804-6354275
$Id$
Linux fv-az1121-699 6.8.0-1029-azure #34~22.04.1-Ubuntu SMP Thu May 1 02:51:54 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux
pid 7438
Current FS Version freesurfer-linux-centos8_x86_64-7.3.2-20220804-6354275
Subject does not have a bstampfile, copying /opt/freesurfer-7.3.2/build-stamp.txt
Subject FS Version: freesurfer-linux-centos8_x86_64-7.3.2-20220804-6354275
No constraints on version because REQ=UnSet and FsVerFile=NotThere
#@#% fs-check-version match = 1
fs-check-version Done
INFO: SUBJECTS_DIR is /tmp/tmps594ishs/freesurfer_output
Actual FREESURFER_HOME /usr/local/freesurfer/7.3.2-1
Linux fv-az1121-699 6.8.0-1029-azure #34~22.04.1-Ubuntu SMP Thu May 1 02:51:54 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux
/tmp/tmps594ishs/freesurfer_output/subjectname
mri_convert /tmp/tmps594ishs/mp2rage.nii /tmp/tmps594ishs/freesurfer_output/subjectname/mri/orig/001.mgz
mri_convert /tmp/tmps594ishs/mp2rage.nii /tmp/tmps594ishs/freesurfer_output/subjectname/mri/orig/001.mgz
reading from /tmp/tmps594ishs/mp2rage.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to /tmp/tmps594ishs/freesurfer_output/subjectname/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Thu Jun 12 21:06:56 UTC 2025
Found 1 runs
/tmp/tmps594ishs/freesurfer_output/subjectname/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
Only one run found so motion
correction will not be performed. I'll
copy the run to rawavg and continue.
cp /tmp/tmps594ishs/freesurfer_output/subjectname/mri/orig/001.mgz /tmp/tmps594ishs/freesurfer_output/subjectname/mri/rawavg.mgz
mri_info /tmp/tmps594ishs/freesurfer_output/subjectname/mri/rawavg.mgz
rawavg.mgz ========================================
Volume information for /tmp/tmps594ishs/freesurfer_output/subjectname/mri/rawavg.mgz
type: MGH
dimensions: 640 x 750 x 800
voxel sizes: 0.300000, 0.300000, 0.300000
type: FLOAT (3)
fov: 240.000
dof: 1
xstart: -96.0, xend: 96.0
ystart: -112.5, yend: 112.5
zstart: -120.0, zend: 120.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.3750
: x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 0.3750
: x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 0.3750
talairach xfm :
Orientation : RAS
Primary Slice Direction: axial
voxel to ras transform:
0.3000 0.0000 0.0000 -95.6250
0.0000 0.3000 0.0000 -112.1250
0.0000 0.0000 0.3000 -119.6250
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0.027
ras to voxel transform:
3.3333 0.0000 0.0000 318.7500
0.0000 3.3333 0.0000 373.7500
0.0000 0.0000 3.3333 398.7500
0.0000 0.0000 0.0000 1.0000
/tmp/tmps594ishs/freesurfer_output/subjectname
mri_convert /tmp/tmps594ishs/freesurfer_output/subjectname/mri/rawavg.mgz /tmp/tmps594ishs/freesurfer_output/subjectname/mri/orig.mgz --conform
mri_convert /tmp/tmps594ishs/freesurfer_output/subjectname/mri/rawavg.mgz /tmp/tmps594ishs/freesurfer_output/subjectname/mri/orig.mgz --conform
reading from /tmp/tmps594ishs/freesurfer_output/subjectname/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 0 255 1000, flo=0, fhi=0.999, dest_type=0
Reslicing using trilinear interpolation
writing to /tmp/tmps594ishs/freesurfer_output/subjectname/mri/orig.mgz...
mri_add_xform_to_header -c /tmp/tmps594ishs/freesurfer_output/subjectname/mri/transforms/talairach.xfm /tmp/tmps594ishs/freesurfer_output/subjectname/mri/orig.mgz /tmp/tmps594ishs/freesurfer_output/subjectname/mri/orig.mgz
INFO: extension is mgz
mri_info /tmp/tmps594ishs/freesurfer_output/subjectname/mri/orig.mgz
orig.mgz ========================================
Volume information for /tmp/tmps594ishs/freesurfer_output/subjectname/mri/orig.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1.000000, 1.000000, 1.000000
type: UCHAR (0)
fov: 256.000
dof: 1
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.3750
: x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.3750
: x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.3750
talairach xfm : /tmp/tmps594ishs/freesurfer_output/subjectname/mri/transforms/talairach.xfm
Orientation : LIA
Primary Slice Direction: coronal
voxel to ras transform:
-1.0000 0.0000 0.0000 128.3750
0.0000 0.0000 1.0000 -127.6250
0.0000 -1.0000 0.0000 128.3750
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-1.0000 -0.0000 -0.0000 128.3750
-0.0000 -0.0000 -1.0000 128.3750
-0.0000 1.0000 -0.0000 127.6250
-0.0000 -0.0000 -0.0000 1.0000
#--------------------------------------------
#@# Talairach Thu Jun 12 21:07:57 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50
/usr/bin/bc
/tmp/tmps594ishs/freesurfer_output/subjectname/mri
/opt/freesurfer-7.3.2/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50
nIters 1
mri_nu_correct.mni 7.3.2
Linux fv-az1121-699 6.8.0-1029-azure #34~22.04.1-Ubuntu SMP Thu May 1 02:51:54 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux
Thu Jun 12 21:07:57 UTC 2025
tmpdir is ./tmp.mri_nu_correct.mni.7800
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.7800/nu0.mgz --dtype uchar
AntsN4BiasFieldCorrectionFs done
mri_convert ./tmp.mri_nu_correct.mni.7800/nu0.mgz orig_nu.mgz --like orig.mgz --conform
mri_convert ./tmp.mri_nu_correct.mni.7800/nu0.mgz orig_nu.mgz --like orig.mgz --conform
reading from ./tmp.mri_nu_correct.mni.7800/nu0.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
writing to orig_nu.mgz...
Thu Jun 12 21:11:02 UTC 2025
mri_nu_correct.mni done
talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
talairach_avi log file is transforms/talairach_avi.log...
mv -f /tmp/tmps594ishs/freesurfer_output/subjectname/mri/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt /tmp/tmps594ishs/freesurfer_output/subjectname/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt
Started at Thu Jun 12 21:11:02 UTC 2025
Ended at Thu Jun 12 21:11:21 UTC 2025
talairach_avi done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
lta_convert --src orig.mgz --trg /opt/freesurfer-7.3.2/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox
7.3.2
--src: orig.mgz src image (geometry).
--trg: /opt/freesurfer-7.3.2/average/mni305.cor.mgz trg image (geometry).
--inmni: transforms/talairach.xfm input MNI/XFM transform.
--outlta: transforms/talairach.xfm.lta output LTA.
--s: fsaverage subject name
--ltavox2vox: output LTA as VOX_TO_VOX transform.
LTA read, type : 1
1.07958 0.00270 -0.01574 0.58327;
0.01399 0.99838 0.31440 -9.30106;
0.00758 -0.40444 1.15055 -29.25244;
0.00000 0.00000 0.00000 1.00000;
setting subject to fsaverage
Writing LTA to file transforms/talairach.xfm.lta...
lta_convert successful.
/tmp/tmps594ishs/freesurfer_output/subjectname/mri/transforms /tmp/tmps594ishs/freesurfer_output/subjectname/mri
/tmp/tmps594ishs/freesurfer_output/subjectname/mri
#--------------------------------------------
#@# Talairach Failure Detection Thu Jun 12 21:11:23 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7053, pval=0.4932 >= threshold=0.0050)
awk -f /opt/freesurfer-7.3.2/bin/extract_talairach_avi_QA.awk /tmp/tmps594ishs/freesurfer_output/subjectname/mri/transforms/talairach_avi.log
tal_QC_AZS /tmp/tmps594ishs/freesurfer_output/subjectname/mri/transforms/talairach_avi.log
TalAviQA: 0.97201
z-score: -1
#--------------------------------------------
#@# Nu Intensity Correction Thu Jun 12 21:11:24 UTC 2025
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4
/usr/bin/bc
/tmp/tmps594ishs/freesurfer_output/subjectname/mri
/opt/freesurfer-7.3.2/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4
nIters 2
mri_nu_correct.mni 7.3.2
Linux fv-az1121-699 6.8.0-1029-azure #34~22.04.1-Ubuntu SMP Thu May 1 02:51:54 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux
Thu Jun 12 21:11:24 UTC 2025
tmpdir is ./tmp.mri_nu_correct.mni.8124
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.8124/nu0.mgz --dtype uchar
AntsN4BiasFieldCorrectionFs done
mri_binarize --i ./tmp.mri_nu_correct.mni.8124/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.8124/ones.mgz
7.3.2
cwd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.8124/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.8124/ones.mgz
sysname Linux
hostname fv-az1121-699
machine x86_64
user runner
input ./tmp.mri_nu_correct.mni.8124/nu0.mgz
frame 0
nErode3d 0
nErode2d 0
output ./tmp.mri_nu_correct.mni.8124/ones.mgz
Binarizing based on threshold
min -1
max +infinity
binval 1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Starting parallel 1
Found 16777216 values in range
Counting number of voxels in first frame
Found 16777215 voxels in final mask
Writing output to ./tmp.mri_nu_correct.mni.8124/ones.mgz
Count: 16777215 16777215.000000 16777216 99.999994
mri_binarize done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.8124/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.8124/sum.junk --avgwf ./tmp.mri_nu_correct.mni.8124/input.mean.dat
7.3.2
cwd
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.8124/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.8124/sum.junk --avgwf ./tmp.mri_nu_correct.mni.8124/input.mean.dat
sysname Linux
hostname fv-az1121-699
machine x86_64
user runner
whitesurfname white
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.8124/ones.mgz
Loading orig.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
Reporting on 1 segmentations
Using PrintSegStat
Computing spatial average of each frame
Writing to ./tmp.mri_nu_correct.mni.8124/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.8124/ones.mgz --i ./tmp.mri_nu_correct.mni.8124/nu0.mgz --sum ./tmp.mri_nu_correct.mni.8124/sum.junk --avgwf ./tmp.mri_nu_correct.mni.8124/output.mean.dat
7.3.2
cwd
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.8124/ones.mgz --i ./tmp.mri_nu_correct.mni.8124/nu0.mgz --sum ./tmp.mri_nu_correct.mni.8124/sum.junk --avgwf ./tmp.mri_nu_correct.mni.8124/output.mean.dat
sysname Linux
hostname fv-az1121-699
machine x86_64
user runner
whitesurfname white
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.8124/ones.mgz
Loading ./tmp.mri_nu_correct.mni.8124/nu0.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
Reporting on 1 segmentations
Using PrintSegStat
Computing spatial average of each frame
Writing to ./tmp.mri_nu_correct.mni.8124/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.8124/nu0.mgz ./tmp.mri_nu_correct.mni.8124/nu0.mgz mul 1.16048835830789136545
Saving result to './tmp.mri_nu_correct.mni.8124/nu0.mgz' (type = MGH )
[ ok ]
mri_convert ./tmp.mri_nu_correct.mni.8124/nu0.mgz nu.mgz --like orig.mgz
mri_convert ./tmp.mri_nu_correct.mni.8124/nu0.mgz nu.mgz --like orig.mgz
reading from ./tmp.mri_nu_correct.mni.8124/nu0.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 4 seconds.
FIRST_PERCENTILE 0.010000
WM_PERCENTILE 0.900000
MAX_R 50.000000
i1 = 6, i2 = 82
#mri_make_uchar# mapping 15 211 to 3 110 : b -5.93289 m 0.548893 : thresh 10.8088 maxsat 475.38 : nzero 12342897 nsat 0
Thu Jun 12 21:14:43 UTC 2025
mri_nu_correct.mni done
mri_add_xform_to_header -c /tmp/tmps594ishs/freesurfer_output/subjectname/mri/transforms/talairach.xfm nu.mgz nu.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Thu Jun 12 21:14:44 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/mri
mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz
using max gradient = 1.000
setting seed for random number genererator to 1234
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading mri_src from nu.mgz...
normalizing image...
NOT doing gentle normalization with control points/label
talairach transform
1.07958 0.00270 -0.01574 0.58327;
0.01399 0.99838 0.31440 -9.30106;
0.00758 -0.40444 1.15055 -29.25244;
0.00000 0.00000 0.00000 1.00000;
processing without aseg, no1d=0
MRInormInit():
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize():
MRIsplineNormalize(): npeaks = 19
Starting OpenSpline(): npoints = 19
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 62 (62), valley at 51 (51)
csf peak at 32, setting threshold to 52
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 65 (65), valley at 53 (53)
csf peak at 33, setting threshold to 54
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 1 minutes and 36 seconds.
#--------------------------------------------
#@# Skull Stripping Thu Jun 12 21:16:21 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/mri
mri_em_register -skull nu.mgz /opt/freesurfer-7.3.2/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta
aligning to atlas containing skull, setting unknown_nbr_spacing = 5
== Number of threads available to mri_em_register for OpenMP = 1 ==
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/opt/freesurfer-7.3.2/average/RB_all_withskull_2020_01_02.gca'...
GCAread took 0 minutes and 2 seconds.
average std = 23.0 using min determinant for regularization = 52.8
0 singular and 9205 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 8.9 or > 556.0
total sample mean = 77.3 (1403 zeros)
************************************************
spacing=8, using 3292 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3292, passno 0, spacing 8
resetting wm mean[0]: 100 --> 108
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=25.0
skull bounding box = (51, 29, 17) --> (205, 241, 220)
finding center of left hemi white matter
using (102, 100, 119) as brain centroid of Right_Cerebral_White_Matter...
MRImask(): AllowDiffGeom = 1
mean wm in atlas = 108, using box (83,74,94) --> (120, 126,144) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 107 +- 3.7
after smoothing, mri peak at 107, scaling input intensities by 1.009
scaling channel 0 by 1.00935
initial log_p = -4.355
************************************************
First Search limited to translation only.
************************************************
max log p = -4.327209 @ (-10.526, 10.526, -10.526)
max log p = -4.238077 @ (5.263, 5.263, 5.263)
max log p = -4.103386 @ (2.632, -2.632, -2.632)
max log p = -4.103386 @ (0.000, 0.000, 0.000)
max log p = -4.087552 @ (-0.658, -0.658, -1.974)
max log p = -4.087552 @ (0.000, 0.000, 0.000)
max log p = -4.087552 @ (0.000, 0.000, 0.000)
max log p = -4.087552 @ (0.000, 0.000, 0.000)
Found translation: (-3.3, 12.5, -9.9): log p = -4.088
****************************************
Nine parameter search. iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.772, old_max_log_p =-4.088 (thresh=-4.1)
1.06375 0.00000 0.00000 -11.47446;
0.00000 1.11081 0.29764 -30.89916;
0.00000 -0.27532 1.02750 26.07788;
0.00000 0.00000 0.00000 1.00000;
iteration took 1 minutes and 10 seconds.
****************************************
Nine parameter search. iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.772, old_max_log_p =-3.772 (thresh=-3.8)
1.06375 0.00000 0.00000 -11.47446;
0.00000 1.11081 0.29764 -30.89916;
0.00000 -0.27532 1.02750 26.07788;
0.00000 0.00000 0.00000 1.00000;
reducing scale to 0.2500
iteration took 1 minutes and 10 seconds.
****************************************
Nine parameter search. iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.654, old_max_log_p =-3.772 (thresh=-3.8)
1.04325 -0.00851 0.03175 -11.59169;
0.00000 1.08921 0.29185 -25.65857;
-0.03480 -0.26485 0.98844 30.03328;
0.00000 0.00000 0.00000 1.00000;
iteration took 1 minutes and 6 seconds.
****************************************
Nine parameter search. iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.648, old_max_log_p =-3.654 (thresh=-3.7)
1.04325 -0.00851 0.03175 -11.59169;
-0.00116 1.10021 0.33011 -31.41711;
-0.03479 -0.30035 0.97836 35.56596;
0.00000 0.00000 0.00000 1.00000;
iteration took 1 minutes and 8 seconds.
****************************************
Nine parameter search. iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.647, old_max_log_p =-3.648 (thresh=-3.6)
1.04383 0.00132 -0.00028 -9.04488;
-0.00118 1.12083 0.33630 -32.79573;
-0.00063 -0.30047 0.97888 31.13393;
0.00000 0.00000 0.00000 1.00000;
reducing scale to 0.0625
iteration took 1 minutes and 9 seconds.
****************************************
Nine parameter search. iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.626, old_max_log_p =-3.647 (thresh=-3.6)
1.04240 0.01742 0.01298 -11.43840;
-0.01818 1.12155 0.31881 -29.55735;
-0.00921 -0.28194 0.98426 28.90162;
0.00000 0.00000 0.00000 1.00000;
iteration took 1 minutes and 1 seconds.
****************************************
Nine parameter search. iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.625, old_max_log_p =-3.626 (thresh=-3.6)
1.04107 0.01509 0.02101 -12.41482;
-0.01816 1.12024 0.31844 -29.82493;
-0.01776 -0.28240 0.98528 29.92633;
0.00000 0.00000 0.00000 1.00000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 3292 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.04107 0.01509 0.02101 -12.41482;
-0.01816 1.12024 0.31844 -29.82493;
-0.01776 -0.28240 0.98528 29.92633;
0.00000 0.00000 0.00000 1.00000;
nsamples 3292
Quasinewton: input matrix
1.04107 0.01509 0.02101 -12.41482;
-0.01816 1.12024 0.31844 -29.82493;
-0.01776 -0.28240 0.98528 29.92633;
0.00000 0.00000 0.00000 1.00000;
IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010
Resulting transform:
1.04107 0.01509 0.02101 -12.41482;
-0.01816 1.12024 0.31844 -29.82493;
-0.01776 -0.28240 0.98528 29.92633;
0.00000 0.00000 0.00000 1.00000;
pass 1, spacing 8: log(p) = -3.625 (old=-4.355)
transform before final EM align:
1.04107 0.01509 0.02101 -12.41482;
-0.01816 1.12024 0.31844 -29.82493;
-0.01776 -0.28240 0.98528 29.92633;
0.00000 0.00000 0.00000 1.00000;
**************************************************
EM alignment process ...
Computing final MAP estimate using 364986 samples.
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.04107 0.01509 0.02101 -12.41482;
-0.01816 1.12024 0.31844 -29.82493;
-0.01776 -0.28240 0.98528 29.92633;
0.00000 0.00000 0.00000 1.00000;
nsamples 364986
Quasinewton: input matrix
1.04107 0.01509 0.02101 -12.41482;
-0.01816 1.12024 0.31844 -29.82493;
-0.01776 -0.28240 0.98528 29.92633;
0.00000 0.00000 0.00000 1.00000;
IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 4.1 tol 0.000000
final transform:
1.04107 0.01509 0.02101 -12.41482;
-0.01816 1.12024 0.31844 -29.82493;
-0.01776 -0.28240 0.98528 29.92633;
0.00000 0.00000 0.00000 1.00000;
writing output transformation to transforms/talairach_with_skull.lta...
#VMPC# mri_em_register VmPeak 800752
FSRUNTIME@ mri_em_register 0.1451 hours 1 threads
registration took 8 minutes and 43 seconds.
mri_watershed -T1 -brain_atlas /opt/freesurfer-7.3.2/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
Mode: T1 normalized volume
Mode: Use the information of atlas (default parms, --help for details)
*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz
Weighting the input with atlas information before watershed
*************************WATERSHED**************************
Sorting...
first estimation of the COG coord: x=129 y=99 z=114 r=79
first estimation of the main basin volume: 2144899 voxels
Looking for seedpoints
2 found in the cerebellum
16 found in the rest of the brain
global maximum in x=106, y=92, z=76, Imax=255
CSF=12, WM_intensity=110, WM_VARIANCE=5
WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110
preflooding height equal to 10 percent
done.
Analyze...
main basin size=9456272073 voxels, voxel volume =1.000
= 9456272073 mmm3 = 9456272.384 cm3
done.
PostAnalyze...Basin Prior
8 basins merged thanks to atlas
***** 0 basin(s) merged in 1 iteration(s)
***** 0 voxel(s) added to the main basin
done.
Weighting the input with prior template
****************TEMPLATE DEFORMATION****************
second estimation of the COG coord: x=128,y=106, z=109, r=9955 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^
GLOBAL CSF_MIN=0, CSF_intensity=7, CSF_MAX=21 , nb = 44406
RIGHT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=11 , nb = 3024
LEFT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=11 , nb = 3060
RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=20 , nb = 18684
LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=21 , nb = 18684
OTHER CSF_MIN=0, CSF_intensity=4, CSF_MAX=14 , nb = 954
Problem with the least square interpolation in GM_MIN calculation.
CSF_MAX TRANSITION GM_MIN GM
GLOBAL
before analyzing : 21, 23, 31, 64
after analyzing : 21, 28, 31, 37
RIGHT_CER
before analyzing : 11, 16, 36, 64
after analyzing : 11, 29, 36, 37
LEFT_CER
before analyzing : 11, 16, 37, 61
after analyzing : 11, 30, 37, 37
RIGHT_BRAIN
before analyzing : 20, 22, 29, 64
after analyzing : 20, 26, 29, 35
LEFT_BRAIN
before analyzing : 21, 24, 32, 64
after analyzing : 21, 29, 32, 37
OTHER
before analyzing : 14, 15, 27, 94
after analyzing : 14, 23, 27, 40
mri_strip_skull: done peeling brain
highly tesselated surface with 10242 vertices
matching...65 iterations
*********************VALIDATION*********************
curvature mean = -0.013, std = 0.011
curvature mean = 69.801, std = 8.241
No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
before rotation: sse = 2.23, sigma = 3.29
after rotation: sse = 2.23, sigma = 3.29
Localization of inacurate regions: Erosion-Dilation steps
the sse mean is 2.27, its var is 2.73
before Erosion-Dilatation 0.09% of inacurate vertices
after Erosion-Dilatation 0.00% of inacurate vertices
Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields
********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...
34 iterations
mri_strip_skull: done peeling brain
Brain Size = 1611792 voxels, voxel volume = 1.000 mm3
= 1611792 mmm3 = 1611.792 cm3
******************************
Saving brainmask.auto.mgz
done
mri_watershed done
cp brainmask.auto.mgz brainmask.mgz
#-------------------------------------
#@# EM Registration Thu Jun 12 21:25:17 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/mri
mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer-7.3.2/average/RB_all_2020-01-02.gca transforms/talairach.lta
setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...
== Number of threads available to mri_em_register for OpenMP = 1 ==
reading 1 input volumes...
logging results to talairach.log
reading '/opt/freesurfer-7.3.2/average/RB_all_2020-01-02.gca'...
GCAread took 0 minutes and 1 seconds.
average std = 7.2 using min determinant for regularization = 5.2
0 singular and 884 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
freeing gibbs priors...
done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 5.9 or > 519.0
total sample mean = 79.1 (1017 zeros)
************************************************
spacing=8, using 2841 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 2841, passno 0, spacing 8
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=20.9
skull bounding box = (62, 44, 31) --> (194, 181, 196)
finding center of left hemi white matter
using (106, 90, 114) as brain centroid of Right_Cerebral_White_Matter...
MRImask(): AllowDiffGeom = 1
mean wm in atlas = 107, using box (90,73,94) --> (122, 106,134) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 107 +- 3.2
after smoothing, mri peak at 107, scaling input intensities by 1.000
scaling channel 0 by 1
initial log_p = -4.170
************************************************
First Search limited to translation only.
************************************************
max log p = -4.041770 @ (-10.526, 10.526, -10.526)
max log p = -3.763349 @ (5.263, 5.263, 5.263)
max log p = -3.695452 @ (2.632, -2.632, -2.632)
max log p = -3.663278 @ (1.316, 3.947, 1.316)
max log p = -3.653469 @ (-0.658, -0.658, -0.658)
max log p = -3.653469 @ (0.000, 0.000, 0.000)
max log p = -3.653469 @ (0.000, 0.000, 0.000)
max log p = -3.653469 @ (0.000, 0.000, 0.000)
Found translation: (-2.0, 16.4, -7.2): log p = -3.653
****************************************
Nine parameter search. iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.190, old_max_log_p =-3.653 (thresh=-3.6)
1.07500 0.00000 0.00000 -11.63188;
0.00000 1.11081 0.29764 -28.48080;
0.00000 -0.25882 0.96593 30.71957;
0.00000 0.00000 0.00000 1.00000;
iteration took 1 minutes and 5 seconds.
****************************************
Nine parameter search. iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.190, old_max_log_p =-3.190 (thresh=-3.2)
1.07500 0.00000 0.00000 -11.63188;
0.00000 1.11081 0.29764 -28.48080;
0.00000 -0.25882 0.96593 30.71957;
0.00000 0.00000 0.00000 1.00000;
reducing scale to 0.2500
iteration took 1 minutes and 0 seconds.
****************************************
Nine parameter search. iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.104, old_max_log_p =-3.190 (thresh=-3.2)
1.05409 0.00000 0.00000 -8.93891;
0.00000 1.15247 0.30880 -34.02222;
0.00000 -0.26367 0.98404 27.44393;
0.00000 0.00000 0.00000 1.00000;
iteration took 0 minutes and 57 seconds.
****************************************
Nine parameter search. iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.104, old_max_log_p =-3.104 (thresh=-3.1)
1.05409 0.00000 0.00000 -8.93891;
0.00000 1.15247 0.30880 -34.02222;
0.00000 -0.26367 0.98404 27.44393;
0.00000 0.00000 0.00000 1.00000;
reducing scale to 0.0625
iteration took 0 minutes and 57 seconds.
****************************************
Nine parameter search. iteration 4 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.052, old_max_log_p =-3.104 (thresh=-3.1)
1.05652 -0.00215 0.00803 -9.89662;
0.00000 1.14977 0.30808 -33.66290;
-0.00863 -0.26274 0.98055 28.36465;
0.00000 0.00000 0.00000 1.00000;
iteration took 0 minutes and 54 seconds.
****************************************
Nine parameter search. iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.052, old_max_log_p =-3.052 (thresh=-3.0)
1.05652 -0.00215 0.00803 -9.89662;
0.00000 1.14977 0.30808 -33.66290;
-0.00863 -0.26274 0.98055 28.36465;
0.00000 0.00000 0.00000 1.00000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 2841 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.05652 -0.00215 0.00803 -9.89662;
0.00000 1.14977 0.30808 -33.66290;
-0.00863 -0.26274 0.98055 28.36465;
0.00000 0.00000 0.00000 1.00000;
nsamples 2841
Quasinewton: input matrix
1.05652 -0.00215 0.00803 -9.89662;
0.00000 1.14977 0.30808 -33.66290;
-0.00863 -0.26274 0.98055 28.36465;
0.00000 0.00000 0.00000 1.00000;
IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010
Resulting transform:
1.05652 -0.00215 0.00803 -9.89662;
0.00000 1.14977 0.30808 -33.66290;
-0.00863 -0.26274 0.98055 28.36465;
0.00000 0.00000 0.00000 1.00000;
pass 1, spacing 8: log(p) = -3.052 (old=-4.170)
transform before final EM align:
1.05652 -0.00215 0.00803 -9.89662;
0.00000 1.14977 0.30808 -33.66290;
-0.00863 -0.26274 0.98055 28.36465;
0.00000 0.00000 0.00000 1.00000;
**************************************************
EM alignment process ...
Computing final MAP estimate using 315638 samples.
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
1.05652 -0.00215 0.00803 -9.89662;
0.00000 1.14977 0.30808 -33.66290;
-0.00863 -0.26274 0.98055 28.36465;
0.00000 0.00000 0.00000 1.00000;
nsamples 315638
Quasinewton: input matrix
1.05652 -0.00215 0.00803 -9.89662;
0.00000 1.14977 0.30808 -33.66290;
-0.00863 -0.26274 0.98055 28.36465;
0.00000 0.00000 0.00000 1.00000;
IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 3.7 tol 0.000000
final transform:
1.05652 -0.00215 0.00803 -9.89662;
0.00000 1.14977 0.30808 -33.66290;
-0.00863 -0.26274 0.98055 28.36465;
0.00000 0.00000 0.00000 1.00000;
writing output transformation to transforms/talairach.lta...
#VMPC# mri_em_register VmPeak 788196
FSRUNTIME@ mri_em_register 0.1087 hours 1 threads
registration took 6 minutes and 31 seconds.
#--------------------------------------
#@# CA Normalize Thu Jun 12 21:31:49 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/mri
mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer-7.3.2/average/RB_all_2020-01-02.gca transforms/talairach.lta norm.mgz
writing control point volume to ctrl_pts.mgz
using MR volume brainmask.mgz to mask input volume...
reading 1 input volume
reading atlas from '/opt/freesurfer-7.3.2/average/RB_all_2020-01-02.gca'...
reading transform from 'transforms/talairach.lta'...
reading input volume from nu.mgz...
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=20.9
skull bounding box = (62, 44, 31) --> (194, 181, 196)
finding center of left hemi white matter
using (106, 90, 114) as brain centroid of Right_Cerebral_White_Matter...
mean wm in atlas = 107, using box (90,73,94) --> (122, 106,134) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 107 +- 3.2
after smoothing, mri peak at 107, scaling input intensities by 1.000
scaling channel 0 by 1
using 246437 sample points...
INFO: compute sample coordinates transform
1.05652 -0.00215 0.00803 -9.89662;
0.00000 1.14977 0.30808 -33.66290;
-0.00863 -0.26274 0.98055 28.36465;
0.00000 0.00000 0.00000 1.00000;
INFO: transform used
finding control points in Left_Cerebral_White_Matter....
found 40230 control points for structure...
bounding box (129, 48, 34) --> (191, 150, 194)
Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0
20 of 9292 (0.2%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39478 control points for structure...
bounding box (67, 47, 32) --> (130, 143, 195)
Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
17 of 9476 (0.2%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3105 control points for structure...
bounding box (130, 124, 62) --> (176, 163, 115)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
0 of 352 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2710 control points for structure...
bounding box (87, 124, 59) --> (128, 162, 115)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
2 of 393 (0.5%) samples deleted
finding control points in Brain_Stem....
found 3475 control points for structure...
bounding box (113, 114, 97) --> (145, 173, 125)
Brain_Stem: limiting intensities to 88.0 --> 132.0
0 of 523 (0.0%) samples deleted
using 20036 total control points for intensity normalization...
bias field = 0.973 +- 0.051
189 of 19997 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 40230 control points for structure...
bounding box (129, 48, 34) --> (191, 150, 194)
Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
30 of 9460 (0.3%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39478 control points for structure...
bounding box (67, 47, 32) --> (130, 143, 195)
Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0
20 of 9622 (0.2%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3105 control points for structure...
bounding box (130, 124, 62) --> (176, 163, 115)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
158 of 479 (33.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2710 control points for structure...
bounding box (87, 124, 59) --> (128, 162, 115)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
157 of 462 (34.0%) samples deleted
finding control points in Brain_Stem....
found 3475 control points for structure...
bounding box (113, 114, 97) --> (145, 173, 125)
Brain_Stem: limiting intensities to 88.0 --> 132.0
40 of 600 (6.7%) samples deleted
using 20623 total control points for intensity normalization...
bias field = 1.029 +- 0.049
175 of 20122 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 40230 control points for structure...
bounding box (129, 48, 34) --> (191, 150, 194)
Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0
21 of 9495 (0.2%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39478 control points for structure...
bounding box (67, 47, 32) --> (130, 143, 195)
Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0
29 of 9631 (0.3%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3105 control points for structure...
bounding box (130, 124, 62) --> (176, 163, 115)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
245 of 503 (48.7%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2710 control points for structure...
bounding box (87, 124, 59) --> (128, 162, 115)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
274 of 465 (58.9%) samples deleted
finding control points in Brain_Stem....
found 3475 control points for structure...
bounding box (113, 114, 97) --> (145, 173, 125)
Brain_Stem: limiting intensities to 88.0 --> 132.0
88 of 638 (13.8%) samples deleted
using 20732 total control points for intensity normalization...
bias field = 1.028 +- 0.043
159 of 19866 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 9 seconds.
#--------------------------------------
#@# CA Reg Thu Jun 12 21:32:58 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/mri
mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer-7.3.2/average/RB_all_2020-01-02.gca transforms/talairach.m3z
not handling expanded ventricles...
using previously computed transform transforms/talairach.lta
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-regularize_mean 0.500
-regularize 0.500
using MR volume brainmask.mgz to mask input volume...
== Number of threads available to mri_ca_register for OpenMP = 1 ==
reading 1 input volumes...
logging results to talairach.log
reading input volume 'norm.mgz'...
reading GCA '/opt/freesurfer-7.3.2/average/RB_all_2020-01-02.gca'...
label assignment complete, 0 changed (0.00%)
freeing gibbs priors...done.
average std[0] = 5.0
Starting GCAMregister()
label assignment complete, 0 changed (0.00%)
npasses = 1, nlevels = 6
#pass# 1 of 1 ************************
enabling zero nodes
setting smoothness cost coefficient to 0.156
#GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.758584
#FOTS# QuadFit found better minimum quadopt=(dt=163.994,rms=0.698519) vs oldopt=(dt=92.48,rms=0.710544)
#GCMRL# 0 dt 163.993517 rms 0.699 7.918% neg 0 invalid 762 tFOTS 9.4440 tGradient 21.6920 tsec 31.8590
#FOTS# QuadFit found better minimum quadopt=(dt=164.117,rms=0.680674) vs oldopt=(dt=92.48,rms=0.684569)
#GCMRL# 1 dt 164.116959 rms 0.681 2.555% neg 0 invalid 762 tFOTS 9.3400 tGradient 21.6480 tsec 31.6990
#FOTS# QuadFit found better minimum quadopt=(dt=166.748,rms=0.672556) vs oldopt=(dt=92.48,rms=0.674419)
#GCMRL# 2 dt 166.748299 rms 0.673 1.193% neg 0 invalid 762 tFOTS 9.4130 tGradient 21.6490 tsec 31.7780
#FOTS# QuadFit found better minimum quadopt=(dt=144.162,rms=0.668033) vs oldopt=(dt=92.48,rms=0.668858)
#GCMRL# 3 dt 144.161616 rms 0.668 0.673% neg 0 invalid 762 tFOTS 9.3000 tGradient 21.7680 tsec 31.7670
#FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.662801) vs oldopt=(dt=369.92,rms=0.662948)
#GCMRL# 4 dt 295.936000 rms 0.663 0.783% neg 0 invalid 762 tFOTS 9.3900 tGradient 21.6870 tsec 31.7790
#FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.659698) vs oldopt=(dt=92.48,rms=0.659772)
#GCMRL# 5 dt 110.976000 rms 0.660 0.468% neg 0 invalid 762 tFOTS 9.9060 tGradient 21.8670 tsec 32.4770
#FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.654475) vs oldopt=(dt=369.92,rms=0.655164)
#GCMRL# 6 dt 517.888000 rms 0.654 0.792% neg 0 invalid 762 tFOTS 9.4190 tGradient 21.9020 tsec 32.0300
#GCMRL# 7 dt 92.480000 rms 0.652 0.346% neg 0 invalid 762 tFOTS 9.9680 tGradient 22.0170 tsec 32.7000
#GCMRL# 8 dt 1479.680000 rms 0.645 1.041% neg 0 invalid 762 tFOTS 9.2960 tGradient 21.8730 tsec 31.8660
#GCMRL# 9 dt 92.480000 rms 0.643 0.305% neg 0 invalid 762 tFOTS 9.4020 tGradient 21.9770 tsec 32.0910
#FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.641752) vs oldopt=(dt=369.92,rms=0.642094)
#GCMRL# 10 dt 517.888000 rms 0.642 0.264% neg 0 invalid 762 tFOTS 10.0250 tGradient 21.7350 tsec 32.4730
#FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.641504) vs oldopt=(dt=92.48,rms=0.641536)
#GCMRL# 11 dt 129.472000 rms 0.642 0.000% neg 0 invalid 762 tFOTS 9.3790 tGradient 21.7340 tsec 31.8410
#GCMRL# 12 dt 129.472000 rms 0.641 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.6930 tsec 22.3930
#GCMRL# 13 dt 129.472000 rms 0.641 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.8400 tsec 22.5560
#GCMRL# 14 dt 129.472000 rms 0.640 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.7990 tsec 22.5100
#GCMRL# 15 dt 129.472000 rms 0.639 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.8270 tsec 22.5540
#GCMRL# 16 dt 129.472000 rms 0.638 0.154% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.7630 tsec 22.4790
#GCMRL# 17 dt 129.472000 rms 0.637 0.159% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.7550 tsec 22.4550
#GCMRL# 18 dt 129.472000 rms 0.636 0.146% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.7490 tsec 22.4450
#GCMRL# 19 dt 129.472000 rms 0.636 0.139% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.4990 tsec 22.1910
#GCMRL# 20 dt 129.472000 rms 0.635 0.145% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.6230 tsec 22.3010
#GCMRL# 21 dt 129.472000 rms 0.634 0.138% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.6620 tsec 22.3520
#GCMRL# 22 dt 129.472000 rms 0.633 0.131% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.7080 tsec 22.4000
#GCMRL# 23 dt 129.472000 rms 0.632 0.122% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.5220 tsec 22.2170
#GCMRL# 24 dt 129.472000 rms 0.631 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.6680 tsec 22.3650
#FOTS# QuadFit found better minimum quadopt=(dt=32.368,rms=0.631477) vs oldopt=(dt=23.12,rms=0.631477)
#GCAMreg# pass 0 level1 5 level2 1 tsec 720.324 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.632139
#FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.630971) vs oldopt=(dt=92.48,rms=0.631031)
#GCMRL# 26 dt 129.472000 rms 0.631 0.185% neg 0 invalid 762 tFOTS 9.1130 tGradient 21.7110 tsec 31.5060
#GCMRL# 27 dt 369.920000 rms 0.630 0.000% neg 0 invalid 762 tFOTS 9.0880 tGradient 21.5730 tsec 31.3540
#GCMRL# 28 dt 369.920000 rms 0.630 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.5900 tsec 22.2750
#GCMRL# 29 dt 369.920000 rms 0.630 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.6280 tsec 22.3150
#GCMRL# 30 dt 369.920000 rms 0.630 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.6470 tsec 22.3330
setting smoothness cost coefficient to 0.615
#GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.638461
#FOTS# QuadFit found better minimum quadopt=(dt=72.716,rms=0.633052) vs oldopt=(dt=103.68,rms=0.633761)
#GCMRL# 32 dt 72.715953 rms 0.633 0.847% neg 0 invalid 762 tFOTS 9.0600 tGradient 12.4350 tsec 22.1710
#FOTS# QuadFit found better minimum quadopt=(dt=217.924,rms=0.626214) vs oldopt=(dt=103.68,rms=0.627862)
#GCMRL# 33 dt 217.924051 rms 0.626 1.080% neg 0 invalid 762 tFOTS 9.5510 tGradient 12.3340 tsec 22.5610
#FOTS# QuadFit found better minimum quadopt=(dt=64.4384,rms=0.622) vs oldopt=(dt=25.92,rms=0.623136)
#GCMRL# 34 dt 64.438356 rms 0.622 0.673% neg 0 invalid 762 tFOTS 9.0330 tGradient 12.4800 tsec 22.1860
#FOTS# QuadFit found better minimum quadopt=(dt=101.517,rms=0.619487) vs oldopt=(dt=103.68,rms=0.619489)
#GCMRL# 35 dt 101.517241 rms 0.619 0.404% neg 0 invalid 762 tFOTS 8.9810 tGradient 12.4540 tsec 22.1110
#FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.618122) vs oldopt=(dt=25.92,rms=0.618385)
#GCMRL# 36 dt 36.288000 rms 0.618 0.000% neg 0 invalid 762 tFOTS 9.0090 tGradient 12.4950 tsec 22.1970
#GCMRL# 37 dt 36.288000 rms 0.617 0.101% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.4830 tsec 13.1660
#GCMRL# 38 dt 36.288000 rms 0.616 0.168% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.4880 tsec 13.1760
#GCMRL# 39 dt 36.288000 rms 0.615 0.233% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.4920 tsec 13.1870
#GCMRL# 40 dt 36.288000 rms 0.613 0.274% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7610 tsec 13.4520
#GCMRL# 41 dt 36.288000 rms 0.612 0.285% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9010 tsec 13.5840
#GCMRL# 42 dt 36.288000 rms 0.610 0.274% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7280 tsec 13.4110
#GCMRL# 43 dt 36.288000 rms 0.608 0.287% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8200 tsec 13.5010
#GCMRL# 44 dt 36.288000 rms 0.607 0.249% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8230 tsec 13.5120
#GCMRL# 45 dt 36.288000 rms 0.605 0.211% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8730 tsec 13.5590
#GCMRL# 46 dt 36.288000 rms 0.604 0.176% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9070 tsec 13.5920
#GCMRL# 47 dt 36.288000 rms 0.604 0.125% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9180 tsec 13.6090
#GCMRL# 48 dt 36.288000 rms 0.603 0.134% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8750 tsec 13.5540
#GCMRL# 49 dt 36.288000 rms 0.602 0.126% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8680 tsec 13.5610
#GCMRL# 50 dt 36.288000 rms 0.601 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9430 tsec 13.6370
#GCMRL# 51 dt 36.288000 rms 0.601 0.067% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9760 tsec 13.6840
#GCMRL# 52 dt 0.450000 rms 0.601 0.000% neg 0 invalid 762 tFOTS 9.2130 tGradient 13.0290 tsec 22.9530
#GCAMreg# pass 0 level1 4 level2 1 tsec 362.365 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.60173
#FOTS# QuadFit found better minimum quadopt=(dt=31.104,rms=0.600725) vs oldopt=(dt=25.92,rms=0.600734)
#GCMRL# 54 dt 31.104000 rms 0.601 0.167% neg 0 invalid 762 tFOTS 9.2520 tGradient 13.0170 tsec 22.9650
setting smoothness cost coefficient to 2.353
#GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.628375
#GCMRL# 56 dt 0.000000 rms 0.628 0.118% neg 0 invalid 762 tFOTS 8.1330 tGradient 8.1030 tsec 16.9430
#GCAMreg# pass 0 level1 3 level2 1 tsec 46.573 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.628375
#GCMRL# 58 dt 0.500000 rms 0.628 0.120% neg 0 invalid 762 tFOTS 8.5230 tGradient 8.0340 tsec 17.2410
#FOTS# QuadFit found better minimum quadopt=(dt=0.075,rms=0.627612) vs oldopt=(dt=0.125,rms=0.627613)
#GCMRL# 59 dt 0.075000 rms 0.628 0.000% neg 0 invalid 762 tFOTS 8.6190 tGradient 8.0750 tsec 17.4010
setting smoothness cost coefficient to 8.000
#GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.706275
#FOTS# QuadFit found better minimum quadopt=(dt=2.36825,rms=0.68245) vs oldopt=(dt=2.88,rms=0.683533)
#GCMRL# 61 dt 2.368248 rms 0.682 3.373% neg 0 invalid 762 tFOTS 8.3970 tGradient 5.6210 tsec 14.6850
#FOTS# QuadFit found better minimum quadopt=(dt=1.75771,rms=0.679391) vs oldopt=(dt=2.88,rms=0.680485)
#GCMRL# 62 dt 1.757709 rms 0.679 0.448% neg 0 invalid 762 tFOTS 8.6160 tGradient 5.5550 tsec 14.8560
#FOTS# QuadFit found better minimum quadopt=(dt=1.42308,rms=0.678637) vs oldopt=(dt=0.72,rms=0.678831)
#GCMRL# 63 dt 1.423077 rms 0.679 0.000% neg 0 invalid 762 tFOTS 8.5730 tGradient 5.6220 tsec 14.9190
#GCMRL# 64 dt 1.423077 rms 0.679 0.013% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.5540 tsec 6.2190
#GCAMreg# pass 0 level1 2 level2 1 tsec 69.654 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.679068
#FOTS# QuadFit found better minimum quadopt=(dt=0.252,rms=0.678531) vs oldopt=(dt=0.18,rms=0.678534)
#GCMRL# 66 dt 0.252000 rms 0.679 0.079% neg 0 invalid 762 tFOTS 8.1560 tGradient 5.5860 tsec 14.4160
#FOTS# QuadFit found better minimum quadopt=(dt=0.1875,rms=0.678516) vs oldopt=(dt=0.18,rms=0.678516)
#GCMRL# 67 dt 0.187500 rms 0.679 0.000% neg 0 invalid 762 tFOTS 8.6040 tGradient 5.6020 tsec 14.9160
setting smoothness cost coefficient to 20.000
#GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.725471
#FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.724815) vs oldopt=(dt=0.08,rms=0.724842)
#GCMRL# 69 dt 0.112000 rms 0.725 0.091% neg 0 invalid 762 tFOTS 8.6730 tGradient 2.3890 tsec 11.7610
#FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.724213) vs oldopt=(dt=0.32,rms=0.724226)
#GCMRL# 70 dt 0.384000 rms 0.724 0.000% neg 0 invalid 762 tFOTS 8.6740 tGradient 2.3820 tsec 11.7610
#GCMRL# 71 dt 0.384000 rms 0.721 0.400% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4140 tsec 3.1040
#GCMRL# 72 dt 0.384000 rms 0.719 0.358% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4240 tsec 3.1290
#GCMRL# 73 dt 0.384000 rms 0.717 0.206% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3580 tsec 3.0470
#GCMRL# 74 dt 0.384000 rms 0.716 0.224% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4150 tsec 3.0970
#GCMRL# 75 dt 0.384000 rms 0.714 0.168% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4100 tsec 3.1030
#GCMRL# 76 dt 0.384000 rms 0.714 -0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4100 tsec 3.7250
#FOTS# QuadFit found better minimum quadopt=(dt=0.768,rms=0.713161) vs oldopt=(dt=1.28,rms=0.713384)
#GCMRL# 77 dt 0.768000 rms 0.713 0.176% neg 0 invalid 762 tFOTS 8.5390 tGradient 2.4030 tsec 11.6060
#FOTS# QuadFit found better minimum quadopt=(dt=0.489247,rms=0.709572) vs oldopt=(dt=0.32,rms=0.710242)
#GCMRL# 78 dt 0.489247 rms 0.710 0.503% neg 0 invalid 762 tFOTS 8.6840 tGradient 2.3980 tsec 11.7690
#FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.709522) vs oldopt=(dt=0.02,rms=0.709528)
#GCMRL# 79 dt 0.028000 rms 0.710 0.000% neg 0 invalid 762 tFOTS 8.7340 tGradient 2.4170 tsec 11.8550
#GCMRL# 80 dt 0.028000 rms 0.710 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4170 tsec 3.0930
#GCAMreg# pass 0 level1 1 level2 1 tsec 96.909 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.709986
#FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.709517) vs oldopt=(dt=0.02,rms=0.709518)
#GCMRL# 82 dt 0.028000 rms 0.710 0.066% neg 0 invalid 762 tFOTS 8.6590 tGradient 2.5210 tsec 11.8600
resetting metric properties...
setting smoothness cost coefficient to 40.000
#GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.682406
#FOTS# QuadFit found better minimum quadopt=(dt=0.229784,rms=0.676832) vs oldopt=(dt=0.32,rms=0.677403)
#GCMRL# 84 dt 0.229784 rms 0.677 0.817% neg 0 invalid 762 tFOTS 8.7460 tGradient 1.9370 tsec 11.3700
#FOTS# QuadFit found better minimum quadopt=(dt=0.024,rms=0.676562) vs oldopt=(dt=0.02,rms=0.676563)
#GCMRL# 85 dt 0.024000 rms 0.677 0.000% neg 0 invalid 762 tFOTS 8.7190 tGradient 1.9220 tsec 11.3660
#GCAMreg# pass 0 level1 0 level2 1 tsec 37.926 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.677038
#FOTS# QuadFit found better minimum quadopt=(dt=0.006,rms=0.676552) vs oldopt=(dt=0.005,rms=0.676552)
#GCMRL# 87 dt 0.006000 rms 0.677 0.072% neg 0 invalid 762 tFOTS 8.7030 tGradient 1.7980 tsec 11.1970
#GCMRL# 88 dt 0.050000 rms 0.677 0.000% neg 0 invalid 762 tFOTS 8.2090 tGradient 1.9350 tsec 10.8430
GCAMregister done in 27.9419 min
Starting GCAmapRenormalizeWithAlignment() without scales
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10253 (16)
mri peak = 0.24309 ( 7)
Left_Lateral_Ventricle (4): linear fit = 0.32 x + 0.0 (1137 voxels, overlap=0.004)
Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1137 voxels, peak = 5), gca=6.4
gca peak = 0.17690 (16)
mri peak = 0.19113 (10)
Right_Lateral_Ventricle (43): linear fit = 0.44 x + 0.0 (993 voxels, overlap=0.172)
Right_Lateral_Ventricle (43): linear fit = 0.44 x + 0.0 (993 voxels, peak = 7), gca=7.0
gca peak = 0.28275 (96)
mri peak = 0.11886 (106)
Right_Pallidum (52): linear fit = 1.10 x + 0.0 (865 voxels, overlap=0.105)
Right_Pallidum (52): linear fit = 1.10 x + 0.0 (865 voxels, peak = 105), gca=105.1
gca peak = 0.18948 (93)
mri peak = 0.10308 (110)
Left_Pallidum (13): linear fit = 1.13 x + 0.0 (790 voxels, overlap=0.030)
Left_Pallidum (13): linear fit = 1.13 x + 0.0 (790 voxels, peak = 106), gca=105.6
gca peak = 0.20755 (55)
mri peak = 0.09290 (56)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (737 voxels, overlap=1.000)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (737 voxels, peak = 55), gca=55.0
gca peak = 0.31831 (58)
mri peak = 0.11220 (60)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (713 voxels, overlap=0.999)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (713 voxels, peak = 59), gca=59.4
gca peak = 0.11957 (102)
mri peak = 0.13750 (102)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (61984 voxels, overlap=0.576)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (61984 voxels, peak = 105), gca=104.5
gca peak = 0.11429 (102)
mri peak = 0.13708 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (64475 voxels, overlap=0.597)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (64475 voxels, peak = 105), gca=104.5
gca peak = 0.14521 (59)
mri peak = 0.03230 (63)
Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (27092 voxels, overlap=0.559)
Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (27092 voxels, peak = 63), gca=63.4
gca peak = 0.14336 (58)
mri peak = 0.03626 (60)
Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (27239 voxels, overlap=0.765)
Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (27239 voxels, peak = 62), gca=62.4
gca peak = 0.13305 (70)
mri peak = 0.12909 (75)
Right_Caudate (50): linear fit = 1.08 x + 0.0 (602 voxels, overlap=0.560)
Right_Caudate (50): linear fit = 1.08 x + 0.0 (602 voxels, peak = 75), gca=75.2
gca peak = 0.15761 (71)
mri peak = 0.11149 (78)
Left_Caudate (11): linear fit = 1.03 x + 0.0 (884 voxels, overlap=0.757)
Left_Caudate (11): linear fit = 1.03 x + 0.0 (884 voxels, peak = 73), gca=73.5
gca peak = 0.13537 (57)
mri peak = 0.04425 (46)
Left_Cerebellum_Cortex (8): linear fit = 0.86 x + 0.0 (20823 voxels, overlap=0.337)
Left_Cerebellum_Cortex (8): linear fit = 0.86 x + 0.0 (20823 voxels, peak = 49), gca=48.7
gca peak = 0.13487 (56)
mri peak = 0.04085 (44)
Right_Cerebellum_Cortex (47): linear fit = 0.82 x + 0.0 (23475 voxels, overlap=0.237)
Right_Cerebellum_Cortex (47): linear fit = 0.82 x + 0.0 (23475 voxels, peak = 46), gca=46.2
gca peak = 0.19040 (84)
mri peak = 0.05880 (87)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (6844 voxels, overlap=0.799)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (6844 voxels, peak = 89), gca=89.5
gca peak = 0.18871 (83)
mri peak = 0.07503 (88)
Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (6722 voxels, overlap=0.828)
Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (6722 voxels, peak = 88), gca=87.6
gca peak = 0.24248 (57)
mri peak = 0.09624 (65)
Left_Amygdala (18): linear fit = 1.10 x + 0.0 (430 voxels, overlap=1.007)
Left_Amygdala (18): linear fit = 1.10 x + 0.0 (430 voxels, peak = 62), gca=62.4
gca peak = 0.35833 (56)
mri peak = 0.10251 (58)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (501 voxels, overlap=0.958)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (501 voxels, peak = 59), gca=58.5
gca peak = 0.12897 (85)
mri peak = 0.06635 (91)
Left_Thalamus (10): linear fit = 1.08 x + 0.0 (5328 voxels, overlap=0.630)
Left_Thalamus (10): linear fit = 1.08 x + 0.0 (5328 voxels, peak = 91), gca=91.4
gca peak = 0.13127 (83)
mri peak = 0.06776 (89)
Right_Thalamus (49): linear fit = 1.12 x + 0.0 (4325 voxels, overlap=0.655)
Right_Thalamus (49): linear fit = 1.12 x + 0.0 (4325 voxels, peak = 93), gca=92.5
gca peak = 0.12974 (78)
mri peak = 0.07627 (84)
Left_Putamen (12): linear fit = 1.12 x + 0.0 (2361 voxels, overlap=0.481)
Left_Putamen (12): linear fit = 1.12 x + 0.0 (2361 voxels, peak = 87), gca=87.0
gca peak = 0.17796 (79)
mri peak = 0.09075 (90)
Right_Putamen (51): linear fit = 1.12 x + 0.0 (2325 voxels, overlap=0.594)
Right_Putamen (51): linear fit = 1.12 x + 0.0 (2325 voxels, peak = 89), gca=88.9
gca peak = 0.10999 (80)
mri peak = 0.06213 (91)
Brain_Stem (16): linear fit = 1.21 x + 0.0 (12102 voxels, overlap=0.417)
Brain_Stem (16): linear fit = 1.21 x + 0.0 (12102 voxels, peak = 96), gca=96.4
gca peak = 0.13215 (88)
mri peak = 0.08770 (101)
Right_VentralDC (60): linear fit = 1.21 x + 0.0 (1248 voxels, overlap=0.036)
Right_VentralDC (60): linear fit = 1.21 x + 0.0 (1248 voxels, peak = 106), gca=106.0
gca peak = 0.11941 (89)
mri peak = 0.09670 (101)
Left_VentralDC (28): linear fit = 1.18 x + 0.0 (1470 voxels, overlap=0.014)
Left_VentralDC (28): linear fit = 1.18 x + 0.0 (1470 voxels, peak = 105), gca=105.5
gca peak = 0.20775 (25)
mri peak = 0.25000 ( 7)
gca peak = 0.13297 (21)
mri peak = 0.54545 ( 6)
gca peak Unknown = 0.94777 ( 0)
gca peak Left_Inf_Lat_Vent = 0.19087 (28)
gca peak Third_Ventricle = 0.20775 (25)
gca peak Fourth_Ventricle = 0.13297 (21)
gca peak CSF = 0.16821 (33)
gca peak Left_Accumbens_area = 0.32850 (63)
gca peak Left_undetermined = 0.98480 (28)
gca peak Left_vessel = 0.40887 (53)
gca peak Left_choroid_plexus = 0.10898 (46)
gca peak Right_Inf_Lat_Vent = 0.17798 (26)
gca peak Right_Accumbens_area = 0.30137 (64)
gca peak Right_vessel = 0.47828 (52)
gca peak Right_choroid_plexus = 0.11612 (45)
gca peak Fifth_Ventricle = 0.59466 (35)
gca peak WM_hypointensities = 0.10053 (78)
gca peak non_WM_hypointensities = 0.07253 (60)
gca peak Optic_Chiasm = 0.25330 (73)
not using caudate to estimate GM means
estimating mean gm scale to be 1.05 x + 0.0
estimating mean wm scale to be 1.02 x + 0.0
estimating mean csf scale to be 0.42 x + 0.0
Left_Pallidum too bright - rescaling by 0.961 (from 1.135) to 101.4 (was 105.6)
Right_Pallidum too bright - rescaling by 0.965 (from 1.095) to 101.4 (was 105.1)
saving intensity scales to talairach.label_intensities.txt
GCAmapRenormalizeWithAlignment() took 2.36592 min
noneg pre
Starting GCAMregister()
label assignment complete, 0 changed (0.00%)
npasses = 1, nlevels = 6
#pass# 1 of 1 ************************
enabling zero nodes
setting smoothness cost coefficient to 0.008
#GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.6806
#FOTS# QuadFit found better minimum quadopt=(dt=139.795,rms=0.668653) vs oldopt=(dt=92.48,rms=0.670174)
#GCMRL# 90 dt 139.795222 rms 0.669 1.755% neg 0 invalid 762 tFOTS 9.1440 tGradient 16.1090 tsec 25.9240
#FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.660309) vs oldopt=(dt=369.92,rms=0.660784)
#GCMRL# 91 dt 295.936000 rms 0.660 1.248% neg 0 invalid 762 tFOTS 8.5410 tGradient 16.2210 tsec 25.4340
#FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.656212) vs oldopt=(dt=92.48,rms=0.656504)
#GCMRL# 92 dt 129.472000 rms 0.656 0.620% neg 0 invalid 762 tFOTS 9.0770 tGradient 16.3990 tsec 26.1690
#FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.653722) vs oldopt=(dt=92.48,rms=0.654172)
#GCMRL# 93 dt 129.472000 rms 0.654 0.379% neg 0 invalid 762 tFOTS 8.9380 tGradient 16.2400 tsec 25.8510
#FOTS# QuadFit found better minimum quadopt=(dt=443.904,rms=0.650128) vs oldopt=(dt=369.92,rms=0.650158)
#GCMRL# 94 dt 443.904000 rms 0.650 0.550% neg 0 invalid 762 tFOTS 9.1000 tGradient 16.2180 tsec 26.0000
#GCMRL# 95 dt 92.480000 rms 0.647 0.487% neg 0 invalid 762 tFOTS 9.5820 tGradient 16.3050 tsec 26.5780
#FOTS# QuadFit found better minimum quadopt=(dt=887.808,rms=0.641934) vs oldopt=(dt=1479.68,rms=0.643048)
#GCMRL# 96 dt 887.808000 rms 0.642 0.777% neg 0 invalid 762 tFOTS 9.0320 tGradient 16.2110 tsec 25.9200
#FOTS# QuadFit found better minimum quadopt=(dt=78.9173,rms=0.639691) vs oldopt=(dt=92.48,rms=0.639697)
#GCMRL# 97 dt 78.917293 rms 0.640 0.349% neg 0 invalid 762 tFOTS 9.5020 tGradient 16.2270 tsec 26.4160
#FOTS# QuadFit found better minimum quadopt=(dt=1183.74,rms=0.637391) vs oldopt=(dt=1479.68,rms=0.637705)
#GCMRL# 98 dt 1183.744000 rms 0.637 0.359% neg 0 invalid 762 tFOTS 8.9990 tGradient 16.2910 tsec 25.9750
#FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.634966) vs oldopt=(dt=92.48,rms=0.635015)
#GCMRL# 99 dt 110.976000 rms 0.635 0.381% neg 0 invalid 762 tFOTS 9.5390 tGradient 16.2220 tsec 26.4490
#FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.634523) vs oldopt=(dt=92.48,rms=0.634569)
#GCMRL# 100 dt 129.472000 rms 0.635 0.070% neg 0 invalid 762 tFOTS 9.0700 tGradient 16.1450 tsec 25.9010
#GCMRL# 101 dt 369.920000 rms 0.634 0.127% neg 0 invalid 762 tFOTS 9.5860 tGradient 16.1810 tsec 26.4500
#FOTS# QuadFit found better minimum quadopt=(dt=73.984,rms=0.633149) vs oldopt=(dt=92.48,rms=0.633153)
#GCMRL# 102 dt 73.984000 rms 0.633 0.090% neg 0 invalid 762 tFOTS 9.0350 tGradient 16.0620 tsec 25.7690
#FOTS# QuadFit found better minimum quadopt=(dt=1183.74,rms=0.631797) vs oldopt=(dt=1479.68,rms=0.631966)
#GCMRL# 103 dt 1183.744000 rms 0.632 0.214% neg 0 invalid 762 tFOTS 9.5450 tGradient 16.0170 tsec 26.2370
#GCMRL# 104 dt 92.480000 rms 0.630 0.249% neg 0 invalid 762 tFOTS 9.4730 tGradient 16.1360 tsec 26.2720
#FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.629901) vs oldopt=(dt=369.92,rms=0.62995)
#GCMRL# 105 dt 295.936000 rms 0.630 0.051% neg 0 invalid 762 tFOTS 9.4800 tGradient 15.9960 tsec 26.1810
#FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.629375) vs oldopt=(dt=92.48,rms=0.62943)
#GCMRL# 106 dt 129.472000 rms 0.629 0.083% neg 0 invalid 762 tFOTS 8.9810 tGradient 16.0900 tsec 25.7490
#FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.629167) vs oldopt=(dt=92.48,rms=0.629196)
#GCMRL# 107 dt 129.472000 rms 0.629 0.000% neg 0 invalid 762 tFOTS 9.5750 tGradient 16.1010 tsec 26.3800
#GCMRL# 108 dt 129.472000 rms 0.629 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 16.1000 tsec 16.7810
#GCMRL# 109 dt 129.472000 rms 0.628 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 16.1660 tsec 16.8380
#GCMRL# 110 dt 129.472000 rms 0.628 0.092% neg 0 invalid 762 tFOTS 0.0000 tGradient 16.1470 tsec 16.8280
#GCMRL# 111 dt 129.472000 rms 0.627 0.109% neg 0 invalid 762 tFOTS 0.0000 tGradient 16.2100 tsec 16.8960
#GCMRL# 112 dt 129.472000 rms 0.626 0.137% neg 0 invalid 762 tFOTS 0.0000 tGradient 16.1370 tsec 16.8070
#GCMRL# 113 dt 129.472000 rms 0.625 0.139% neg 0 invalid 762 tFOTS 0.0000 tGradient 16.1100 tsec 16.7960
#GCMRL# 114 dt 129.472000 rms 0.624 0.148% neg 0 invalid 762 tFOTS 0.0000 tGradient 16.1450 tsec 16.8170
#GCMRL# 115 dt 129.472000 rms 0.624 0.149% neg 0 invalid 762 tFOTS 0.0000 tGradient 16.1350 tsec 16.7960
#GCMRL# 116 dt 129.472000 rms 0.623 0.140% neg 0 invalid 762 tFOTS 0.0000 tGradient 15.9380 tsec 16.6090
#GCMRL# 117 dt 129.472000 rms 0.622 0.155% neg 0 invalid 762 tFOTS 0.0000 tGradient 16.1450 tsec 16.8240
#GCMRL# 118 dt 129.472000 rms 0.621 0.150% neg 0 invalid 762 tFOTS 0.0000 tGradient 16.1580 tsec 16.8300
#GCMRL# 119 dt 129.472000 rms 0.620 0.129% neg 0 invalid 762 tFOTS 0.0000 tGradient 16.1160 tsec 16.7740
#GCMRL# 120 dt 129.472000 rms 0.619 0.139% neg 0 invalid 762 tFOTS 0.0000 tGradient 16.0770 tsec 16.7650
#GCMRL# 121 dt 129.472000 rms 0.618 0.141% neg 0 invalid 762 tFOTS 0.0000 tGradient 16.0050 tsec 16.6710
#GCMRL# 122 dt 129.472000 rms 0.617 0.135% neg 0 invalid 762 tFOTS 0.0000 tGradient 16.1650 tsec 16.8360
#GCMRL# 123 dt 129.472000 rms 0.617 0.114% neg 0 invalid 762 tFOTS 0.0000 tGradient 15.9950 tsec 16.6630
#GCMRL# 124 dt 129.472000 rms 0.616 0.120% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.3520 tsec 23.0300
#GCMRL# 125 dt 129.472000 rms 0.615 0.142% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2710 tsec 22.9470
#GCMRL# 126 dt 129.472000 rms 0.614 0.137% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.3630 tsec 23.0340
#GCMRL# 127 dt 129.472000 rms 0.613 0.134% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5510 tsec 23.2280
#GCMRL# 128 dt 129.472000 rms 0.613 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.3370 tsec 23.0030
#GCMRL# 129 dt 129.472000 rms 0.612 0.100% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2060 tsec 22.8930
#GCMRL# 130 dt 129.472000 rms 0.611 0.124% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.3110 tsec 22.9630
#GCMRL# 131 dt 129.472000 rms 0.611 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2290 tsec 22.8950
#GCMRL# 132 dt 129.472000 rms 0.610 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.1620 tsec 22.8240
#GCMRL# 133 dt 129.472000 rms 0.609 0.100% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2040 tsec 22.8850
#GCMRL# 134 dt 129.472000 rms 0.609 0.084% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.4470 tsec 23.1250
#GCMRL# 135 dt 129.472000 rms 0.608 0.099% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2830 tsec 22.9690
#GCMRL# 136 dt 129.472000 rms 0.608 0.084% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.4160 tsec 23.0890
#GCMRL# 137 dt 129.472000 rms 0.607 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.3870 tsec 23.0580
#GCMRL# 138 dt 129.472000 rms 0.607 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.3950 tsec 23.0660
#GCMRL# 139 dt 129.472000 rms 0.606 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5490 tsec 23.2420
#GCMRL# 140 dt 129.472000 rms 0.606 0.088% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5330 tsec 23.2190
#GCMRL# 141 dt 129.472000 rms 0.605 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5900 tsec 23.2800
#GCMRL# 142 dt 129.472000 rms 0.605 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.7020 tsec 23.4150
#GCMRL# 143 dt 129.472000 rms 0.605 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.8320 tsec 23.5320
#GCMRL# 144 dt 129.472000 rms 0.604 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.9090 tsec 23.6040
#GCMRL# 145 dt 129.472000 rms 0.604 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.6940 tsec 23.3800
#GCMRL# 146 dt 129.472000 rms 0.603 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.4850 tsec 23.1650
#GCMRL# 147 dt 129.472000 rms 0.603 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.1710 tsec 22.8640
#GCMRL# 148 dt 129.472000 rms 0.602 0.071% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.1910 tsec 22.8730
#GCMRL# 149 dt 129.472000 rms 0.602 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2440 tsec 22.9320
#GCMRL# 150 dt 129.472000 rms 0.602 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2440 tsec 22.9140
#GCMRL# 151 dt 129.472000 rms 0.602 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.1910 tsec 22.8860
#GCMRL# 152 dt 129.472000 rms 0.601 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2110 tsec 22.8840
#GCMRL# 153 dt 129.472000 rms 0.601 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.1640 tsec 22.8280
#GCMRL# 154 dt 129.472000 rms 0.601 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.3840 tsec 23.0610
#GCMRL# 155 dt 129.472000 rms 0.600 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5350 tsec 23.1980
#GCMRL# 156 dt 129.472000 rms 0.600 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.4590 tsec 23.1200
#GCMRL# 157 dt 129.472000 rms 0.600 0.054% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5260 tsec 23.2020
#GCMRL# 158 dt 129.472000 rms 0.599 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.4040 tsec 23.0750
#GCMRL# 159 dt 129.472000 rms 0.599 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2330 tsec 22.9110
#GCMRL# 160 dt 129.472000 rms 0.599 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.4390 tsec 23.1110
#GCMRL# 161 dt 129.472000 rms 0.599 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5230 tsec 23.1990
#GCMRL# 162 dt 129.472000 rms 0.599 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.4620 tsec 23.1360
#GCMRL# 163 dt 129.472000 rms 0.598 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.3590 tsec 23.0170
#GCMRL# 164 dt 129.472000 rms 0.598 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5820 tsec 23.2450
#GCMRL# 165 dt 129.472000 rms 0.598 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5120 tsec 23.1910
#GCMRL# 166 dt 129.472000 rms 0.598 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.6480 tsec 23.3290
#GCMRL# 167 dt 129.472000 rms 0.597 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5280 tsec 23.1990
#GCMRL# 168 dt 129.472000 rms 0.597 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.4330 tsec 23.1000
#GCMRL# 169 dt 129.472000 rms 0.597 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.4870 tsec 23.1640
#GCMRL# 170 dt 129.472000 rms 0.597 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.4970 tsec 23.1570
#GCMRL# 171 dt 129.472000 rms 0.596 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5410 tsec 23.2120
#GCMRL# 172 dt 129.472000 rms 0.596 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5050 tsec 23.1710
#GCMRL# 173 dt 129.472000 rms 0.596 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.4420 tsec 23.1250
#GCMRL# 174 dt 129.472000 rms 0.596 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.4430 tsec 23.1190
#GCMRL# 175 dt 129.472000 rms 0.596 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.4660 tsec 23.1340
#GCMRL# 176 dt 129.472000 rms 0.595 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.3330 tsec 23.0060
#GCMRL# 177 dt 129.472000 rms 0.595 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2160 tsec 22.8890
#GCMRL# 178 dt 129.472000 rms 0.595 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5560 tsec 23.2150
#GCMRL# 179 dt 129.472000 rms 0.595 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5040 tsec 23.1580
#GCMRL# 180 dt 129.472000 rms 0.595 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.3950 tsec 23.0640
#GCMRL# 181 dt 129.472000 rms 0.595 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.3930 tsec 23.0660
#GCMRL# 182 dt 129.472000 rms 0.595 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.4710 tsec 23.1480
#GCMRL# 183 dt 129.472000 rms 0.594 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5540 tsec 23.2280
#GCMRL# 184 dt 129.472000 rms 0.594 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.4190 tsec 23.0960
#GCMRL# 185 dt 129.472000 rms 0.594 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2440 tsec 22.9140
#GCMRL# 186 dt 129.472000 rms 0.594 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2070 tsec 22.8770
#GCMRL# 187 dt 129.472000 rms 0.594 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2720 tsec 22.9420
#GCMRL# 188 dt 129.472000 rms 0.593 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2630 tsec 22.9190
#GCMRL# 189 dt 129.472000 rms 0.593 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.1820 tsec 22.8440
#GCMRL# 190 dt 129.472000 rms 0.593 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2190 tsec 22.8780
#GCMRL# 191 dt 129.472000 rms 0.593 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.3430 tsec 23.0110
#GCMRL# 192 dt 129.472000 rms 0.593 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2890 tsec 22.9530
#GCMRL# 193 dt 129.472000 rms 0.593 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.1740 tsec 22.8360
#GCMRL# 194 dt 129.472000 rms 0.593 0.016% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2270 tsec 22.8860
#GCMRL# 195 dt 129.472000 rms 0.592 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.1000 tsec 22.7580
#GCMRL# 196 dt 129.472000 rms 0.592 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.1960 tsec 22.8710
#FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.592305) vs oldopt=(dt=369.92,rms=0.592314)
#GCMRL# 197 dt 517.888000 rms 0.592 0.000% neg 0 invalid 762 tFOTS 9.3650 tGradient 22.2000 tsec 32.2380
#GCAMreg# pass 0 level1 5 level2 1 tsec 2489.73 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.592976
#GCMRL# 199 dt 369.920000 rms 0.591 0.362% neg 0 invalid 762 tFOTS 8.8480 tGradient 22.1830 tsec 31.6900
#FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.590529) vs oldopt=(dt=92.48,rms=0.590554)
#GCMRL# 200 dt 129.472000 rms 0.591 0.051% neg 0 invalid 762 tFOTS 8.9340 tGradient 22.2210 tsec 31.8160
#FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.590044) vs oldopt=(dt=369.92,rms=0.59011)
#GCMRL# 201 dt 517.888000 rms 0.590 0.082% neg 0 invalid 762 tFOTS 9.4340 tGradient 22.1210 tsec 32.2250
#FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.589824) vs oldopt=(dt=92.48,rms=0.589841)
#GCMRL# 202 dt 129.472000 rms 0.590 0.000% neg 0 invalid 762 tFOTS 8.8990 tGradient 22.3060 tsec 31.8810
#GCMRL# 203 dt 129.472000 rms 0.590 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2080 tsec 22.8740
#GCMRL# 204 dt 129.472000 rms 0.589 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2500 tsec 22.9210
#GCMRL# 205 dt 129.472000 rms 0.589 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5190 tsec 23.2020
#GCMRL# 206 dt 129.472000 rms 0.589 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5050 tsec 23.1780
#GCMRL# 207 dt 129.472000 rms 0.589 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.4540 tsec 23.1250
#GCMRL# 208 dt 129.472000 rms 0.588 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.4890 tsec 23.1630
#GCMRL# 209 dt 129.472000 rms 0.588 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5200 tsec 23.1950
#GCMRL# 210 dt 129.472000 rms 0.588 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.3060 tsec 22.9700
#GCMRL# 211 dt 129.472000 rms 0.588 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.3410 tsec 23.0080
#GCMRL# 212 dt 129.472000 rms 0.588 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5350 tsec 23.2070
#GCMRL# 213 dt 129.472000 rms 0.588 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.4640 tsec 23.1320
#GCMRL# 214 dt 129.472000 rms 0.587 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.4480 tsec 23.1350
#GCMRL# 215 dt 369.920000 rms 0.587 0.023% neg 0 invalid 762 tFOTS 9.5120 tGradient 22.5340 tsec 32.7200
#FOTS# QuadFit found better minimum quadopt=(dt=32.368,rms=0.587309) vs oldopt=(dt=23.12,rms=0.587313)
#GCMRL# 216 dt 32.368000 rms 0.587 0.000% neg 0 invalid 762 tFOTS 10.0550 tGradient 22.5330 tsec 33.2850
#GCMRL# 217 dt 32.368000 rms 0.587 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.3740 tsec 23.0410
#GCMRL# 218 dt 32.368000 rms 0.587 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5190 tsec 23.1920
setting smoothness cost coefficient to 0.031
#GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.58983
#FOTS# QuadFit found better minimum quadopt=(dt=156.781,rms=0.585278) vs oldopt=(dt=103.68,rms=0.585659)
#GCMRL# 220 dt 156.781065 rms 0.585 0.772% neg 0 invalid 762 tFOTS 8.9910 tGradient 12.9660 tsec 22.6220
#FOTS# QuadFit found better minimum quadopt=(dt=207.515,rms=0.577415) vs oldopt=(dt=103.68,rms=0.579197)
#GCMRL# 221 dt 207.515152 rms 0.577 1.344% neg 0 invalid 762 tFOTS 9.0080 tGradient 12.9150 tsec 22.5940
#FOTS# QuadFit found better minimum quadopt=(dt=64,rms=0.573321) vs oldopt=(dt=25.92,rms=0.574334)
#GCMRL# 222 dt 64.000000 rms 0.573 0.709% neg 0 invalid 762 tFOTS 8.9650 tGradient 12.9220 tsec 22.5600
#FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.570234) vs oldopt=(dt=103.68,rms=0.570602)
#GCMRL# 223 dt 145.152000 rms 0.570 0.538% neg 0 invalid 762 tFOTS 8.4140 tGradient 12.9210 tsec 21.9970
#FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.567687) vs oldopt=(dt=103.68,rms=0.568579)
#GCMRL# 224 dt 62.208000 rms 0.568 0.447% neg 0 invalid 762 tFOTS 9.0470 tGradient 12.7230 tsec 22.4620
#FOTS# QuadFit found better minimum quadopt=(dt=113.672,rms=0.565925) vs oldopt=(dt=103.68,rms=0.565929)
#GCMRL# 225 dt 113.671642 rms 0.566 0.310% neg 0 invalid 762 tFOTS 9.0120 tGradient 12.7190 tsec 22.3990
#FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.564047) vs oldopt=(dt=25.92,rms=0.564412)
#GCMRL# 226 dt 36.288000 rms 0.564 0.332% neg 0 invalid 762 tFOTS 9.0210 tGradient 12.7260 tsec 22.4320
#FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.554882) vs oldopt=(dt=414.72,rms=0.556925)
#GCMRL# 227 dt 580.608000 rms 0.555 1.625% neg 0 invalid 762 tFOTS 8.5230 tGradient 12.7840 tsec 21.9910
#FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.55334) vs oldopt=(dt=25.92,rms=0.553672)
#GCMRL# 228 dt 36.288000 rms 0.553 0.278% neg 0 invalid 762 tFOTS 8.9910 tGradient 12.8000 tsec 22.4760
#FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.551974) vs oldopt=(dt=103.68,rms=0.552189)
#GCMRL# 229 dt 145.152000 rms 0.552 0.247% neg 0 invalid 762 tFOTS 9.1030 tGradient 12.8810 tsec 22.6630
#FOTS# QuadFit found better minimum quadopt=(dt=77.848,rms=0.550892) vs oldopt=(dt=103.68,rms=0.550996)
#GCMRL# 230 dt 77.847953 rms 0.551 0.196% neg 0 invalid 762 tFOTS 9.5190 tGradient 12.9680 tsec 23.1700
#FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.550122) vs oldopt=(dt=103.68,rms=0.550172)
#GCMRL# 231 dt 82.944000 rms 0.550 0.140% neg 0 invalid 762 tFOTS 9.0500 tGradient 12.9100 tsec 22.6320
#FOTS# QuadFit found better minimum quadopt=(dt=79.4161,rms=0.549216) vs oldopt=(dt=103.68,rms=0.549297)
#GCMRL# 232 dt 79.416058 rms 0.549 0.165% neg 0 invalid 762 tFOTS 9.6060 tGradient 12.8700 tsec 23.1480
#FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.548731) vs oldopt=(dt=25.92,rms=0.548831)
#GCMRL# 233 dt 36.288000 rms 0.549 0.088% neg 0 invalid 762 tFOTS 8.5270 tGradient 12.8910 tsec 22.1020
#FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.545387) vs oldopt=(dt=414.72,rms=0.546)
#GCMRL# 234 dt 580.608000 rms 0.545 0.609% neg 0 invalid 762 tFOTS 9.1180 tGradient 12.8890 tsec 22.6930
#FOTS# QuadFit found better minimum quadopt=(dt=67.2593,rms=0.543626) vs oldopt=(dt=103.68,rms=0.544153)
#GCMRL# 235 dt 67.259259 rms 0.544 0.323% neg 0 invalid 762 tFOTS 9.0930 tGradient 12.9020 tsec 22.6670
#FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.543101) vs oldopt=(dt=103.68,rms=0.543167)
#GCMRL# 236 dt 82.944000 rms 0.543 0.097% neg 0 invalid 762 tFOTS 9.0550 tGradient 12.8710 tsec 22.6060
#FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.542423) vs oldopt=(dt=103.68,rms=0.542478)
#GCMRL# 237 dt 82.944000 rms 0.542 0.125% neg 0 invalid 762 tFOTS 9.0400 tGradient 12.7380 tsec 22.4510
#FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.542141) vs oldopt=(dt=25.92,rms=0.542193)
#GCMRL# 238 dt 36.288000 rms 0.542 0.052% neg 0 invalid 762 tFOTS 9.0890 tGradient 12.8060 tsec 22.5820
#GCMRL# 239 dt 1658.880000 rms 0.537 0.923% neg 0 invalid 762 tFOTS 9.1810 tGradient 12.9300 tsec 22.8000
#FOTS# QuadFit found better minimum quadopt=(dt=69.8182,rms=0.534) vs oldopt=(dt=103.68,rms=0.534844)
#GCMRL# 240 dt 69.818182 rms 0.534 0.584% neg 0 invalid 762 tFOTS 9.1220 tGradient 12.9380 tsec 22.7450
#FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.533615) vs oldopt=(dt=25.92,rms=0.533669)
#GCMRL# 241 dt 36.288000 rms 0.534 0.072% neg 0 invalid 762 tFOTS 9.0800 tGradient 12.9460 tsec 22.7050
#FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.533199) vs oldopt=(dt=103.68,rms=0.533246)
#GCMRL# 242 dt 145.152000 rms 0.533 0.078% neg 0 invalid 762 tFOTS 9.0340 tGradient 12.8500 tsec 22.5880
#FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.532682) vs oldopt=(dt=103.68,rms=0.532732)
#GCMRL# 243 dt 82.944000 rms 0.533 0.097% neg 0 invalid 762 tFOTS 9.0910 tGradient 12.8690 tsec 22.6500
#FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.532493) vs oldopt=(dt=25.92,rms=0.532519)
#GCMRL# 244 dt 36.288000 rms 0.532 0.000% neg 0 invalid 762 tFOTS 9.1020 tGradient 12.9010 tsec 22.6950
#GCMRL# 245 dt 36.288000 rms 0.532 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8590 tsec 13.5470
#GCMRL# 246 dt 36.288000 rms 0.532 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8720 tsec 13.5450
#GCMRL# 247 dt 36.288000 rms 0.532 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8530 tsec 13.5210
#GCMRL# 248 dt 36.288000 rms 0.532 0.069% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8940 tsec 13.5920
#GCMRL# 249 dt 36.288000 rms 0.531 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8190 tsec 13.4920
#GCMRL# 250 dt 36.288000 rms 0.531 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7540 tsec 13.4290
#GCMRL# 251 dt 36.288000 rms 0.530 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7090 tsec 13.3910
#GCMRL# 252 dt 36.288000 rms 0.530 0.082% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7680 tsec 13.4580
#GCMRL# 253 dt 36.288000 rms 0.529 0.094% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8080 tsec 13.5040
#GCMRL# 254 dt 36.288000 rms 0.529 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7660 tsec 13.4570
#GCMRL# 255 dt 36.288000 rms 0.528 0.116% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7660 tsec 13.4380
#GCMRL# 256 dt 36.288000 rms 0.527 0.121% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8790 tsec 13.5460
#GCMRL# 257 dt 36.288000 rms 0.527 0.121% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9380 tsec 13.6010
#GCMRL# 258 dt 36.288000 rms 0.526 0.106% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9870 tsec 13.6640
#GCMRL# 259 dt 36.288000 rms 0.526 0.110% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0380 tsec 13.7090
#GCMRL# 260 dt 36.288000 rms 0.525 0.107% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0030 tsec 13.6860
#GCMRL# 261 dt 36.288000 rms 0.525 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0370 tsec 13.7040
#GCMRL# 262 dt 36.288000 rms 0.524 0.094% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9730 tsec 13.6350
#GCMRL# 263 dt 36.288000 rms 0.524 0.088% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8320 tsec 13.5010
#GCMRL# 264 dt 36.288000 rms 0.523 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8360 tsec 13.4970
#GCMRL# 265 dt 36.288000 rms 0.523 0.092% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8200 tsec 13.4820
#GCMRL# 266 dt 36.288000 rms 0.522 0.090% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8400 tsec 13.5010
#GCMRL# 267 dt 36.288000 rms 0.522 0.093% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8910 tsec 13.5620
#GCMRL# 268 dt 36.288000 rms 0.521 0.096% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9600 tsec 13.6280
#GCMRL# 269 dt 36.288000 rms 0.521 0.084% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9150 tsec 13.5830
#GCMRL# 270 dt 36.288000 rms 0.520 0.075% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9050 tsec 13.5760
#GCMRL# 271 dt 36.288000 rms 0.520 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8000 tsec 13.4660
#GCMRL# 272 dt 36.288000 rms 0.520 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9340 tsec 13.5850
#GCMRL# 273 dt 36.288000 rms 0.519 0.083% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7840 tsec 13.4550
#GCMRL# 274 dt 36.288000 rms 0.519 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7660 tsec 13.4240
#GCMRL# 275 dt 36.288000 rms 0.518 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7780 tsec 13.4280
#GCMRL# 276 dt 36.288000 rms 0.518 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8620 tsec 13.5340
#GCMRL# 277 dt 36.288000 rms 0.518 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7670 tsec 13.4290
#GCMRL# 278 dt 36.288000 rms 0.518 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7830 tsec 13.4430
#GCMRL# 279 dt 36.288000 rms 0.517 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8800 tsec 13.5600
#GCMRL# 280 dt 36.288000 rms 0.517 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0360 tsec 13.7270
#GCMRL# 281 dt 36.288000 rms 0.517 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9880 tsec 13.6430
#GCMRL# 282 dt 36.288000 rms 0.516 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9180 tsec 13.5870
#GCMRL# 283 dt 36.288000 rms 0.516 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0020 tsec 13.6650
#GCMRL# 284 dt 36.288000 rms 0.516 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9620 tsec 13.6260
#GCMRL# 285 dt 36.288000 rms 0.515 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9630 tsec 13.6270
#GCMRL# 286 dt 36.288000 rms 0.515 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9670 tsec 13.6260
#GCMRL# 287 dt 36.288000 rms 0.515 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0060 tsec 13.6710
#GCMRL# 288 dt 36.288000 rms 0.515 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9610 tsec 13.6310
#GCMRL# 289 dt 36.288000 rms 0.515 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9790 tsec 13.6470
#GCMRL# 290 dt 36.288000 rms 0.514 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8900 tsec 13.5490
#GCMRL# 291 dt 36.288000 rms 0.514 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9700 tsec 13.6360
#GCMRL# 292 dt 36.288000 rms 0.514 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9670 tsec 13.6220
#GCMRL# 293 dt 36.288000 rms 0.514 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8970 tsec 13.5540
#GCMRL# 294 dt 36.288000 rms 0.514 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9290 tsec 13.5820
#GCMRL# 295 dt 36.288000 rms 0.513 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8800 tsec 13.5530
#GCMRL# 296 dt 36.288000 rms 0.513 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0290 tsec 13.6840
#GCMRL# 297 dt 36.288000 rms 0.513 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9840 tsec 13.6400
#GCMRL# 298 dt 36.288000 rms 0.513 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9340 tsec 13.5890
#GCMRL# 299 dt 36.288000 rms 0.513 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9000 tsec 13.5660
#GCMRL# 300 dt 36.288000 rms 0.512 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8700 tsec 13.5330
#GCMRL# 301 dt 36.288000 rms 0.512 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8520 tsec 13.5170
#GCMRL# 302 dt 36.288000 rms 0.512 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8670 tsec 13.5310
#GCMRL# 303 dt 36.288000 rms 0.512 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9060 tsec 13.5760
#GCMRL# 304 dt 36.288000 rms 0.512 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8880 tsec 13.5540
#GCMRL# 305 dt 36.288000 rms 0.512 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0200 tsec 13.6830
#GCMRL# 306 dt 36.288000 rms 0.512 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9260 tsec 13.5900
#GCMRL# 307 dt 36.288000 rms 0.511 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9050 tsec 13.5630
#GCMRL# 308 dt 36.288000 rms 0.511 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7820 tsec 13.4400
#GCMRL# 309 dt 36.288000 rms 0.511 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7680 tsec 13.4260
#GCMRL# 310 dt 36.288000 rms 0.511 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7630 tsec 13.4270
#GCMRL# 311 dt 36.288000 rms 0.511 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7320 tsec 13.3900
#GCMRL# 312 dt 36.288000 rms 0.511 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9060 tsec 13.5680
#GCMRL# 313 dt 36.288000 rms 0.511 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9010 tsec 13.5720
#GCMRL# 314 dt 36.288000 rms 0.510 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8180 tsec 13.4860
#GCMRL# 315 dt 36.288000 rms 0.510 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7130 tsec 13.3890
#FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.510125) vs oldopt=(dt=103.68,rms=0.510161)
#GCMRL# 316 dt 145.152000 rms 0.510 0.055% neg 0 invalid 762 tFOTS 8.8800 tGradient 12.7730 tsec 22.3120
#FOTS# QuadFit found better minimum quadopt=(dt=9.072,rms=0.510125) vs oldopt=(dt=6.48,rms=0.510128)
#GCMRL# 317 dt 9.072000 rms 0.510 0.000% neg 0 invalid 762 tFOTS 8.8840 tGradient 12.7000 tsec 22.8590
#GCMRL# 318 dt 9.072000 rms 0.510 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7830 tsec 13.4390
#GCAMreg# pass 0 level1 4 level2 1 tsec 1611.5 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.510875
#FOTS# QuadFit found better minimum quadopt=(dt=115.469,rms=0.508374) vs oldopt=(dt=103.68,rms=0.508378)
#GCMRL# 320 dt 115.468531 rms 0.508 0.490% neg 0 invalid 762 tFOTS 9.4700 tGradient 12.7920 tsec 22.9300
#FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.507497) vs oldopt=(dt=25.92,rms=0.507669)
#GCMRL# 321 dt 36.288000 rms 0.507 0.172% neg 0 invalid 762 tFOTS 8.4220 tGradient 12.8120 tsec 21.8980
#FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.506808) vs oldopt=(dt=103.68,rms=0.506945)
#GCMRL# 322 dt 145.152000 rms 0.507 0.136% neg 0 invalid 762 tFOTS 8.9430 tGradient 12.7730 tsec 22.3890
#FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.506307) vs oldopt=(dt=103.68,rms=0.506332)
#GCMRL# 323 dt 82.944000 rms 0.506 0.099% neg 0 invalid 762 tFOTS 9.0040 tGradient 12.9300 tsec 22.6030
#FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.506184) vs oldopt=(dt=25.92,rms=0.506193)
#GCMRL# 324 dt 36.288000 rms 0.506 0.000% neg 0 invalid 762 tFOTS 9.4380 tGradient 12.9340 tsec 23.0550
#GCMRL# 325 dt 36.288000 rms 0.506 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8160 tsec 13.4800
#GCMRL# 326 dt 36.288000 rms 0.506 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7220 tsec 13.3790
#GCMRL# 327 dt 36.288000 rms 0.506 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8590 tsec 13.5280
#GCMRL# 328 dt 36.288000 rms 0.505 0.054% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8800 tsec 13.5440
#GCMRL# 329 dt 36.288000 rms 0.505 0.069% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8760 tsec 13.5460
#GCMRL# 330 dt 36.288000 rms 0.505 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8990 tsec 13.5680
#GCMRL# 331 dt 36.288000 rms 0.504 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9400 tsec 13.6180
#GCMRL# 332 dt 36.288000 rms 0.504 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8900 tsec 13.5650
#GCMRL# 333 dt 36.288000 rms 0.504 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9740 tsec 13.6410
#GCMRL# 334 dt 36.288000 rms 0.504 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8600 tsec 13.5290
#GCMRL# 335 dt 36.288000 rms 0.503 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8850 tsec 13.5580
#GCMRL# 336 dt 36.288000 rms 0.503 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9230 tsec 13.5940
#GCMRL# 337 dt 36.288000 rms 0.503 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9100 tsec 13.5810
#GCMRL# 338 dt 36.288000 rms 0.503 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9000 tsec 13.5720
#GCMRL# 339 dt 36.288000 rms 0.502 0.054% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8840 tsec 13.5510
#GCMRL# 340 dt 36.288000 rms 0.502 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8760 tsec 13.5370
#GCMRL# 341 dt 36.288000 rms 0.502 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8090 tsec 13.4780
#GCMRL# 342 dt 36.288000 rms 0.502 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8170 tsec 13.4850
#GCMRL# 343 dt 36.288000 rms 0.501 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8440 tsec 13.5110
#GCMRL# 344 dt 36.288000 rms 0.501 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9080 tsec 13.5790
#GCMRL# 345 dt 36.288000 rms 0.501 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8260 tsec 13.5120
#GCMRL# 346 dt 36.288000 rms 0.501 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7380 tsec 13.4160
#GCMRL# 347 dt 36.288000 rms 0.501 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8670 tsec 13.5430
#GCMRL# 348 dt 36.288000 rms 0.500 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7440 tsec 13.4100
#GCMRL# 349 dt 36.288000 rms 0.500 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7990 tsec 13.4660
#GCMRL# 350 dt 36.288000 rms 0.500 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7670 tsec 13.4350
#GCMRL# 351 dt 36.288000 rms 0.500 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7130 tsec 13.3850
#GCMRL# 352 dt 36.288000 rms 0.500 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7710 tsec 13.4440
#GCMRL# 353 dt 36.288000 rms 0.500 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8100 tsec 13.4880
#GCMRL# 354 dt 36.288000 rms 0.500 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8290 tsec 13.5030
#GCMRL# 355 dt 36.288000 rms 0.499 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7340 tsec 13.4050
#GCMRL# 356 dt 36.288000 rms 0.499 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7460 tsec 13.4130
#GCMRL# 357 dt 36.288000 rms 0.499 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9120 tsec 13.5740
#GCMRL# 358 dt 36.288000 rms 0.499 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7430 tsec 13.4050
#GCMRL# 359 dt 36.288000 rms 0.499 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7270 tsec 13.3840
#GCMRL# 360 dt 36.288000 rms 0.499 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7550 tsec 13.4240
#GCMRL# 361 dt 36.288000 rms 0.499 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8040 tsec 13.4780
#GCMRL# 362 dt 36.288000 rms 0.498 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8820 tsec 13.5510
#GCMRL# 363 dt 36.288000 rms 0.498 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8660 tsec 13.5510
#FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.498249) vs oldopt=(dt=103.68,rms=0.498259)
#GCMRL# 364 dt 62.208000 rms 0.498 0.000% neg 0 invalid 762 tFOTS 8.8330 tGradient 12.8290 tsec 22.3370
#GCMRL# 365 dt 62.208000 rms 0.498 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8700 tsec 13.5280
#GCMRL# 366 dt 62.208000 rms 0.498 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8400 tsec 13.4980
#GCMRL# 367 dt 62.208000 rms 0.498 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8760 tsec 13.5360
setting smoothness cost coefficient to 0.118
#GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.509209
#FOTS# QuadFit found better minimum quadopt=(dt=23,rms=0.507552) vs oldopt=(dt=32,rms=0.50775)
#GCMRL# 369 dt 23.000000 rms 0.508 0.325% neg 0 invalid 762 tFOTS 8.8090 tGradient 7.9400 tsec 17.4080
#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.506084) vs oldopt=(dt=32,rms=0.506238)
#GCMRL# 370 dt 44.800000 rms 0.506 0.289% neg 0 invalid 762 tFOTS 8.2490 tGradient 7.8950 tsec 16.7940
#FOTS# QuadFit found better minimum quadopt=(dt=94.6087,rms=0.503948) vs oldopt=(dt=32,rms=0.50453)
#GCMRL# 371 dt 94.608696 rms 0.504 0.422% neg 0 invalid 762 tFOTS 8.7590 tGradient 7.8690 tsec 17.2810
#FOTS# QuadFit found better minimum quadopt=(dt=35.2711,rms=0.500346) vs oldopt=(dt=32,rms=0.500346)
#GCMRL# 372 dt 35.271111 rms 0.500 0.715% neg 0 invalid 762 tFOTS 8.2510 tGradient 7.9620 tsec 16.8640
#FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.498996) vs oldopt=(dt=32,rms=0.499012)
#GCMRL# 373 dt 38.400000 rms 0.499 0.270% neg 0 invalid 762 tFOTS 8.3000 tGradient 7.9330 tsec 16.8910
#FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.497041) vs oldopt=(dt=32,rms=0.497145)
#GCMRL# 374 dt 38.400000 rms 0.497 0.392% neg 0 invalid 762 tFOTS 8.2740 tGradient 7.9750 tsec 16.9080
#FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.496371) vs oldopt=(dt=32,rms=0.496441)
#GCMRL# 375 dt 25.600000 rms 0.496 0.135% neg 0 invalid 762 tFOTS 8.2750 tGradient 7.8690 tsec 16.8020
#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.49469) vs oldopt=(dt=32,rms=0.495015)
#GCMRL# 376 dt 44.800000 rms 0.495 0.339% neg 0 invalid 762 tFOTS 8.3110 tGradient 7.9150 tsec 16.8820
#FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.494218) vs oldopt=(dt=32,rms=0.494242)
#GCMRL# 377 dt 25.600000 rms 0.494 0.095% neg 0 invalid 762 tFOTS 8.3280 tGradient 7.9500 tsec 16.9370
#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.49293) vs oldopt=(dt=32,rms=0.493188)
#GCMRL# 378 dt 44.800000 rms 0.493 0.261% neg 0 invalid 762 tFOTS 8.2920 tGradient 7.9290 tsec 16.8720
#FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.492541) vs oldopt=(dt=32,rms=0.492576)
#GCMRL# 379 dt 25.600000 rms 0.493 0.079% neg 0 invalid 762 tFOTS 8.2530 tGradient 7.8920 tsec 16.8000
#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.491364) vs oldopt=(dt=32,rms=0.491524)
#GCMRL# 380 dt 44.800000 rms 0.491 0.239% neg 0 invalid 762 tFOTS 8.7860 tGradient 7.8790 tsec 17.3320
#FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.491054) vs oldopt=(dt=8,rms=0.491117)
#GCMRL# 381 dt 11.200000 rms 0.491 0.063% neg 0 invalid 762 tFOTS 8.2960 tGradient 7.8880 tsec 16.8360
#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.490527) vs oldopt=(dt=32,rms=0.490592)
#GCMRL# 382 dt 44.800000 rms 0.491 0.107% neg 0 invalid 762 tFOTS 8.2650 tGradient 7.8740 tsec 16.7930
#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.489446) vs oldopt=(dt=32,rms=0.489571)
#GCMRL# 383 dt 44.800000 rms 0.489 0.221% neg 0 invalid 762 tFOTS 8.7870 tGradient 7.8490 tsec 17.2860
#FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.489184) vs oldopt=(dt=8,rms=0.489243)
#GCMRL# 384 dt 11.200000 rms 0.489 0.053% neg 0 invalid 762 tFOTS 8.2550 tGradient 7.8120 tsec 16.7180
#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.488658) vs oldopt=(dt=32,rms=0.48874)
#GCMRL# 385 dt 44.800000 rms 0.489 0.108% neg 0 invalid 762 tFOTS 8.2310 tGradient 7.8240 tsec 16.7040
#FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.487978) vs oldopt=(dt=32,rms=0.487989)
#GCMRL# 386 dt 38.400000 rms 0.488 0.139% neg 0 invalid 762 tFOTS 8.7390 tGradient 7.8090 tsec 17.1980
#FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.487699) vs oldopt=(dt=32,rms=0.487782)
#GCMRL# 387 dt 19.200000 rms 0.488 0.057% neg 0 invalid 762 tFOTS 8.2470 tGradient 7.7750 tsec 16.6720
#FOTS# QuadFit found better minimum quadopt=(dt=409.6,rms=0.485709) vs oldopt=(dt=512,rms=0.485764)
#GCMRL# 388 dt 409.600000 rms 0.486 0.408% neg 0 invalid 762 tFOTS 8.7240 tGradient 7.8360 tsec 17.2150
#GCMRL# 389 dt 32.000000 rms 0.484 0.317% neg 0 invalid 762 tFOTS 8.2290 tGradient 8.1390 tsec 17.0190
#FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.483185) vs oldopt=(dt=32,rms=0.483254)
#GCMRL# 390 dt 38.400000 rms 0.483 0.204% neg 0 invalid 762 tFOTS 8.7640 tGradient 8.0470 tsec 17.4630
#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.482337) vs oldopt=(dt=32,rms=0.482434)
#GCMRL# 391 dt 44.800000 rms 0.482 0.176% neg 0 invalid 762 tFOTS 8.2440 tGradient 7.8200 tsec 16.7170
#FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.481884) vs oldopt=(dt=32,rms=0.481886)
#GCMRL# 392 dt 25.600000 rms 0.482 0.094% neg 0 invalid 762 tFOTS 8.2750 tGradient 8.0180 tsec 16.9500
#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.481628) vs oldopt=(dt=32,rms=0.481662)
#GCMRL# 393 dt 44.800000 rms 0.482 0.053% neg 0 invalid 762 tFOTS 8.2530 tGradient 7.8580 tsec 16.7670
#GCMRL# 394 dt 32.000000 rms 0.481 0.053% neg 0 invalid 762 tFOTS 8.7660 tGradient 7.8730 tsec 17.2970
#FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.481192) vs oldopt=(dt=32,rms=0.481214)
#GCMRL# 395 dt 25.600000 rms 0.481 0.000% neg 0 invalid 762 tFOTS 8.7680 tGradient 7.8900 tsec 17.3540
#GCMRL# 396 dt 25.600000 rms 0.481 0.015% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.9490 tsec 8.6040
#GCMRL# 397 dt 25.600000 rms 0.481 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8030 tsec 8.4570
#GCMRL# 398 dt 25.600000 rms 0.480 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8270 tsec 8.4840
#GCMRL# 399 dt 25.600000 rms 0.480 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8330 tsec 8.4890
#GCMRL# 400 dt 25.600000 rms 0.479 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8950 tsec 8.5480
#GCMRL# 401 dt 25.600000 rms 0.479 0.116% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.9720 tsec 8.6280
#GCMRL# 402 dt 25.600000 rms 0.478 0.131% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8320 tsec 8.4850
#GCMRL# 403 dt 25.600000 rms 0.477 0.155% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8540 tsec 8.5080
#GCMRL# 404 dt 25.600000 rms 0.477 0.112% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8600 tsec 8.5380
#GCMRL# 405 dt 25.600000 rms 0.476 0.146% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.9100 tsec 8.5820
#GCMRL# 406 dt 25.600000 rms 0.476 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8730 tsec 8.5460
#GCMRL# 407 dt 25.600000 rms 0.475 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8310 tsec 8.5040
#GCMRL# 408 dt 25.600000 rms 0.475 0.115% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7970 tsec 8.4690
#GCMRL# 409 dt 25.600000 rms 0.474 0.142% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7540 tsec 8.4300
#GCMRL# 410 dt 25.600000 rms 0.474 0.130% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7920 tsec 8.4660
#GCMRL# 411 dt 25.600000 rms 0.473 0.087% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7520 tsec 8.4280
#GCMRL# 412 dt 25.600000 rms 0.473 -0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8580 tsec 9.1630
#FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.473133) vs oldopt=(dt=8,rms=0.47314)
#GCMRL# 413 dt 11.200000 rms 0.473 0.009% neg 0 invalid 762 tFOTS 9.1680 tGradient 7.8920 tsec 17.7320
#GCMRL# 414 dt 32.000000 rms 0.473 0.029% neg 0 invalid 762 tFOTS 8.5920 tGradient 7.8080 tsec 17.0740
#FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.472969) vs oldopt=(dt=32,rms=0.472976)
#GCAMreg# pass 0 level1 3 level2 1 tsec 667.928 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.473628
#FOTS# QuadFit found better minimum quadopt=(dt=80.8989,rms=0.469444) vs oldopt=(dt=32,rms=0.470339)
#GCMRL# 416 dt 80.898876 rms 0.469 0.883% neg 0 invalid 762 tFOTS 9.1600 tGradient 7.8960 tsec 17.7330
#FOTS# QuadFit found better minimum quadopt=(dt=24.1717,rms=0.468538) vs oldopt=(dt=32,rms=0.46869)
#GCMRL# 417 dt 24.171674 rms 0.469 0.193% neg 0 invalid 762 tFOTS 8.6530 tGradient 7.8470 tsec 17.1830
#FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.468213) vs oldopt=(dt=32,rms=0.468216)
#GCMRL# 418 dt 38.400000 rms 0.468 0.069% neg 0 invalid 762 tFOTS 8.5960 tGradient 7.8610 tsec 17.1310
#FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.468077) vs oldopt=(dt=32,rms=0.468108)
#GCMRL# 419 dt 19.200000 rms 0.468 0.000% neg 0 invalid 762 tFOTS 8.5960 tGradient 7.8330 tsec 17.1160
#GCMRL# 420 dt 19.200000 rms 0.468 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7820 tsec 8.4570
#GCMRL# 421 dt 19.200000 rms 0.468 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8320 tsec 8.5030
#GCMRL# 422 dt 19.200000 rms 0.467 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8440 tsec 8.5150
#GCMRL# 423 dt 19.200000 rms 0.467 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8340 tsec 8.5140
#GCMRL# 424 dt 19.200000 rms 0.467 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7780 tsec 8.4480
#GCMRL# 425 dt 19.200000 rms 0.466 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8020 tsec 8.4850
#GCMRL# 426 dt 19.200000 rms 0.466 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7820 tsec 8.4580
#GCMRL# 427 dt 19.200000 rms 0.466 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8020 tsec 8.4750
#GCMRL# 428 dt 19.200000 rms 0.465 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7800 tsec 8.4520
#GCMRL# 429 dt 19.200000 rms 0.465 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7720 tsec 8.4590
#GCMRL# 430 dt 19.200000 rms 0.465 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7860 tsec 8.4550
#GCMRL# 431 dt 19.200000 rms 0.464 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7610 tsec 8.4350
#GCMRL# 432 dt 19.200000 rms 0.464 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7610 tsec 8.4130
#GCMRL# 433 dt 19.200000 rms 0.464 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7680 tsec 8.4180
#GCMRL# 434 dt 19.200000 rms 0.464 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8220 tsec 8.4660
#GCMRL# 435 dt 19.200000 rms 0.463 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8010 tsec 8.4450
#GCMRL# 436 dt 19.200000 rms 0.463 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7650 tsec 8.4140
#GCMRL# 437 dt 19.200000 rms 0.463 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7830 tsec 8.4370
#GCMRL# 438 dt 19.200000 rms 0.463 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7430 tsec 8.3940
#GCMRL# 439 dt 19.200000 rms 0.463 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7860 tsec 8.4380
#GCMRL# 440 dt 19.200000 rms 0.463 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7710 tsec 8.4230
#GCMRL# 441 dt 19.200000 rms 0.462 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8290 tsec 8.4780
#GCMRL# 442 dt 19.200000 rms 0.462 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7820 tsec 8.4300
#GCMRL# 443 dt 19.200000 rms 0.462 -0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7880 tsec 9.0440
#FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.462012) vs oldopt=(dt=32,rms=0.462015)
#GCMRL# 444 dt 38.400000 rms 0.462 0.023% neg 0 invalid 762 tFOTS 8.2140 tGradient 7.7680 tsec 16.6330
#FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.461955) vs oldopt=(dt=8,rms=0.46197)
setting smoothness cost coefficient to 0.400
#GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.485295
#GCMRL# 446 dt 0.000000 rms 0.485 0.128% neg 0 invalid 762 tFOTS 8.2540 tGradient 5.2900 tsec 14.1970
#GCMRL# 447 dt 0.150000 rms 0.485 0.000% neg 0 invalid 762 tFOTS 8.2870 tGradient 5.3240 tsec 14.8860
#GCAMreg# pass 0 level1 2 level2 1 tsec 47.596 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.485295
#GCMRL# 449 dt 0.000000 rms 0.485 0.128% neg 0 invalid 762 tFOTS 8.2620 tGradient 5.3000 tsec 14.2190
#GCMRL# 450 dt 0.150000 rms 0.485 0.000% neg 0 invalid 762 tFOTS 8.2650 tGradient 5.3060 tsec 14.8370
setting smoothness cost coefficient to 1.000
#GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.530295
#GCMRL# 452 dt 1.280000 rms 0.527 0.634% neg 0 invalid 762 tFOTS 8.2390 tGradient 2.1450 tsec 11.0400
#FOTS# QuadFit found better minimum quadopt=(dt=0.064,rms=0.526903) vs oldopt=(dt=0.08,rms=0.526903)
#GCMRL# 453 dt 0.064000 rms 0.527 0.000% neg 0 invalid 762 tFOTS 8.2320 tGradient 2.1440 tsec 11.0420
#GCAMreg# pass 0 level1 1 level2 1 tsec 37.438 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.527486
#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.526684) vs oldopt=(dt=0.32,rms=0.526705)
#GCMRL# 455 dt 0.448000 rms 0.527 0.152% neg 0 invalid 762 tFOTS 8.2330 tGradient 2.1900 tsec 11.0750
#GCMRL# 456 dt 0.080000 rms 0.527 0.000% neg 0 invalid 762 tFOTS 8.2440 tGradient 2.1600 tsec 11.0710
#GCMRL# 457 dt 0.080000 rms 0.527 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1380 tsec 2.7880
resetting metric properties...
setting smoothness cost coefficient to 2.000
#GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.470002
#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.456551) vs oldopt=(dt=0.32,rms=0.46005)
#GCMRL# 459 dt 0.448000 rms 0.457 2.862% neg 0 invalid 762 tFOTS 7.7370 tGradient 1.6370 tsec 10.0310
#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.454157) vs oldopt=(dt=0.32,rms=0.45483)
#GCMRL# 460 dt 0.448000 rms 0.454 0.524% neg 0 invalid 762 tFOTS 7.7570 tGradient 1.6850 tsec 10.0930
#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.452642) vs oldopt=(dt=0.32,rms=0.453058)
#GCMRL# 461 dt 0.448000 rms 0.453 0.334% neg 0 invalid 762 tFOTS 7.7280 tGradient 1.6390 tsec 10.0210
#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.45174) vs oldopt=(dt=0.32,rms=0.451997)
#GCMRL# 462 dt 0.448000 rms 0.452 0.199% neg 0 invalid 762 tFOTS 7.7240 tGradient 1.6590 tsec 10.0370
#FOTS# QuadFit found better minimum quadopt=(dt=0.458333,rms=0.45102) vs oldopt=(dt=0.32,rms=0.45123)
#GCMRL# 463 dt 0.458333 rms 0.451 0.159% neg 0 invalid 762 tFOTS 7.7680 tGradient 1.6600 tsec 10.0820
#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.450522) vs oldopt=(dt=0.32,rms=0.450659)
#GCMRL# 464 dt 0.448000 rms 0.451 0.111% neg 0 invalid 762 tFOTS 7.6960 tGradient 1.7120 tsec 10.0560
#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.450085) vs oldopt=(dt=0.32,rms=0.450201)
#GCMRL# 465 dt 0.448000 rms 0.450 0.097% neg 0 invalid 762 tFOTS 7.7190 tGradient 1.6380 tsec 10.0090
#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.449786) vs oldopt=(dt=0.32,rms=0.44987)
#GCMRL# 466 dt 0.448000 rms 0.450 0.066% neg 0 invalid 762 tFOTS 7.7010 tGradient 1.6830 tsec 10.0360
#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.449478) vs oldopt=(dt=0.32,rms=0.449555)
#GCMRL# 467 dt 0.448000 rms 0.449 0.068% neg 0 invalid 762 tFOTS 7.7360 tGradient 1.6590 tsec 10.0510
#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.449275) vs oldopt=(dt=0.32,rms=0.449329)
#GCMRL# 468 dt 0.448000 rms 0.449 0.000% neg 0 invalid 762 tFOTS 7.7380 tGradient 1.6890 tsec 10.0950
#GCMRL# 469 dt 0.448000 rms 0.449 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6380 tsec 2.2880
#GCMRL# 470 dt 0.448000 rms 0.449 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6990 tsec 2.3480
#GCMRL# 471 dt 0.448000 rms 0.448 0.094% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.7050 tsec 2.3540
#GCMRL# 472 dt 0.448000 rms 0.448 0.096% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6350 tsec 2.2850
#GCMRL# 473 dt 0.448000 rms 0.447 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6550 tsec 2.3070
#GCMRL# 474 dt 0.448000 rms 0.447 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6330 tsec 2.2870
#GCMRL# 475 dt 0.448000 rms 0.447 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6340 tsec 2.2840
#GCMRL# 476 dt 0.448000 rms 0.447 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6810 tsec 2.3350
#GCMRL# 477 dt 0.448000 rms 0.447 -0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6760 tsec 3.1800
#FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.446836) vs oldopt=(dt=0.08,rms=0.446836)
#GCMRL# 478 dt 0.112000 rms 0.447 0.001% neg 0 invalid 762 tFOTS 7.6790 tGradient 1.6780 tsec 10.0110
#FOTS# QuadFit found better minimum quadopt=(dt=0.064,rms=0.44684) vs oldopt=(dt=0.08,rms=0.44684)
#GCAMreg# pass 0 level1 0 level2 1 tsec 154.769 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00
tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.447587
#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.443597) vs oldopt=(dt=0.32,rms=0.444475)
#GCMRL# 480 dt 0.448000 rms 0.444 0.891% neg 0 invalid 762 tFOTS 7.6920 tGradient 1.7190 tsec 10.0600
#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.443144) vs oldopt=(dt=0.32,rms=0.443265)
#GCMRL# 481 dt 0.448000 rms 0.443 0.102% neg 0 invalid 762 tFOTS 7.6840 tGradient 1.6370 tsec 9.9690
#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.442984) vs oldopt=(dt=0.32,rms=0.443023)
#GCMRL# 482 dt 0.448000 rms 0.443 0.000% neg 0 invalid 762 tFOTS 7.7090 tGradient 1.6300 tsec 10.0020
#GCMRL# 483 dt 0.448000 rms 0.443 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6540 tsec 2.3030
#GCMRL# 484 dt 0.448000 rms 0.443 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6540 tsec 2.3020
#GCMRL# 485 dt 0.448000 rms 0.443 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6580 tsec 2.5610
GCAMregister done in 111.506 min
********************* ALLOWING NEGATIVE NODES IN DEFORMATION********************************
noneg post
Starting GCAMregister()
label assignment complete, 0 changed (0.00%)
npasses = 1, nlevels = 6
#pass# 1 of 1 ************************
enabling zero nodes
setting smoothness cost coefficient to 0.008
#GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.441636
#GCMRL# 487 dt 0.000000 rms 0.441 0.164% neg 0 invalid 762 tFOTS 9.2370 tGradient 21.9450 tsec 31.8330
#GCAMreg# pass 0 level1 5 level2 1 tsec 76.174 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.441636
#FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.440537) vs oldopt=(dt=369.92,rms=0.440559)
#GCMRL# 489 dt 295.936000 rms 0.441 0.249% neg 0 invalid 762 tFOTS 9.2230 tGradient 22.0240 tsec 31.8960
#FOTS# QuadFit found better minimum quadopt=(dt=32.368,rms=0.440489) vs oldopt=(dt=23.12,rms=0.440497)
#GCMRL# 490 dt 32.368000 rms 0.440 0.000% neg 0 invalid 762 tFOTS 9.7510 tGradient 22.0320 tsec 32.4510
#GCMRL# 491 dt 32.368000 rms 0.440 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2770 tsec 22.9290
#GCMRL# 492 dt 32.368000 rms 0.440 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2230 tsec 22.8770
#GCMRL# 493 dt 32.368000 rms 0.440 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.1060 tsec 22.7590
#GCMRL# 494 dt 32.368000 rms 0.440 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.0430 tsec 22.6900
#GCMRL# 495 dt 32.368000 rms 0.440 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.0520 tsec 22.7020
#GCMRL# 496 dt 32.368000 rms 0.440 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.1310 tsec 22.7820
setting smoothness cost coefficient to 0.031
#GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.440894
#FOTS# QuadFit found better minimum quadopt=(dt=9.072,rms=0.440119) vs oldopt=(dt=6.48,rms=0.440123)
#GCMRL# 498 dt 9.072000 rms 0.440 0.176% neg 0 invalid 762 tFOTS 9.7650 tGradient 12.7930 tsec 23.2130
#FOTS# QuadFit found better minimum quadopt=(dt=9.072,rms=0.440099) vs oldopt=(dt=6.48,rms=0.440104)
#GCMRL# 499 dt 9.072000 rms 0.440 0.000% neg 0 invalid 762 tFOTS 9.7630 tGradient 12.7440 tsec 23.1760
#GCMRL# 500 dt 9.072000 rms 0.440 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7590 tsec 13.4060
#GCAMreg# pass 0 level1 4 level2 1 tsec 86.048 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.440843
#FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.437637) vs oldopt=(dt=103.68,rms=0.438117)
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
#GCMRL# 502 dt 145.152000 rms 0.438 0.727% neg 0 invalid 762 tFOTS 9.2650 tGradient 12.7390 tsec 23.2770
#FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.437455) vs oldopt=(dt=25.92,rms=0.437473)
#GCMRL# 503 dt 36.288000 rms 0.437 0.000% neg 0 invalid 762 tFOTS 9.2850 tGradient 12.7370 tsec 22.6910
#GCMRL# 504 dt 36.288000 rms 0.437 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7140 tsec 13.3680
#GCMRL# 505 dt 36.288000 rms 0.437 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7400 tsec 13.3960
#GCMRL# 506 dt 36.288000 rms 0.437 0.096% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.6870 tsec 13.3390
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
#GCMRL# 507 dt 36.288000 rms 0.436 0.128% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.7200 tsec 14.0110
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
#GCMRL# 508 dt 36.288000 rms 0.435 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.5850 tsec 13.8630
#GCMRL# 509 dt 36.288000 rms 0.435 0.123% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.6740 tsec 13.3280
iter 0, gcam->neg = 2
after 7 iterations, nbhd size=1, neg = 0
#GCMRL# 510 dt 36.288000 rms 0.435 0.093% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9340 tsec 16.3320
#FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.434557) vs oldopt=(dt=25.92,rms=0.43456)
setting smoothness cost coefficient to 0.118
#GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.435641
#FOTS# QuadFit found better minimum quadopt=(dt=30.2959,rms=0.433782) vs oldopt=(dt=32,rms=0.433795)
iter 0, gcam->neg = 4
after 7 iterations, nbhd size=1, neg = 0
#GCMRL# 512 dt 30.295858 rms 0.434 0.420% neg 0 invalid 762 tFOTS 9.7590 tGradient 7.7900 tsec 20.9260
#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.432413) vs oldopt=(dt=32,rms=0.432535)
iter 0, gcam->neg = 4
after 0 iterations, nbhd size=0, neg = 0
#GCMRL# 513 dt 44.800000 rms 0.432 0.323% neg 0 invalid 762 tFOTS 9.8130 tGradient 7.8140 tsec 18.9580
#FOTS# QuadFit found better minimum quadopt=(dt=22.2762,rms=0.431624) vs oldopt=(dt=32,rms=0.431815)
#GCMRL# 514 dt 22.276243 rms 0.432 0.000% neg 0 invalid 762 tFOTS 9.7970 tGradient 7.8040 tsec 18.2740
#GCMRL# 515 dt 22.276243 rms 0.431 0.138% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8010 tsec 8.4560
iter 0, gcam->neg = 2
after 7 iterations, nbhd size=1, neg = 0
#GCMRL# 516 dt 22.276243 rms 0.430 0.194% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8190 tsec 11.3390
#GCMRL# 517 dt 22.276243 rms 0.429 0.192% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7320 tsec 8.3830
iter 0, gcam->neg = 3
after 0 iterations, nbhd size=0, neg = 0
#GCMRL# 518 dt 22.276243 rms 0.429 0.199% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7210 tsec 8.9990
iter 0, gcam->neg = 1
after 6 iterations, nbhd size=1, neg = 0
#GCMRL# 519 dt 22.276243 rms 0.428 0.141% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7040 tsec 10.7410
iter 0, gcam->neg = 6
after 10 iterations, nbhd size=1, neg = 0
#GCMRL# 520 dt 22.276243 rms 0.427 0.176% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6990 tsec 11.9070
#GCMRL# 521 dt 22.276243 rms 0.427 0.143% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7150 tsec 8.3640
iter 0, gcam->neg = 6
after 11 iterations, nbhd size=1, neg = 0
#GCMRL# 522 dt 22.276243 rms 0.426 0.088% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7020 tsec 12.2140
iter 0, gcam->neg = 2
after 2 iterations, nbhd size=0, neg = 0
#GCMRL# 523 dt 22.276243 rms 0.426 0.141% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7920 tsec 9.6810
#GCMRL# 524 dt 22.276243 rms 0.425 0.130% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7560 tsec 8.4040
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
#GCMRL# 525 dt 22.276243 rms 0.425 0.100% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7660 tsec 9.0480
iter 0, gcam->neg = 3
after 8 iterations, nbhd size=1, neg = 0
#GCMRL# 526 dt 22.276243 rms 0.424 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7430 tsec 11.4000
#FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.42397) vs oldopt=(dt=32,rms=0.423973)
#GCMRL# 527 dt 25.600000 rms 0.424 0.089% neg 0 invalid 762 tFOTS 9.7850 tGradient 7.7410 tsec 18.1810
#FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.423915) vs oldopt=(dt=8,rms=0.423917)
#GCMRL# 528 dt 11.200000 rms 0.424 0.000% neg 0 invalid 762 tFOTS 9.8050 tGradient 7.7090 tsec 18.1800
#GCMRL# 529 dt 11.200000 rms 0.424 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7070 tsec 8.3620
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
#GCMRL# 530 dt 11.200000 rms 0.424 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7210 tsec 9.0000
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
#GCMRL# 531 dt 11.200000 rms 0.424 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7020 tsec 8.9820
iter 0, gcam->neg = 1
after 6 iterations, nbhd size=1, neg = 0
#GCAMreg# pass 0 level1 3 level2 1 tsec 262.532 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.42429
#FOTS# QuadFit found better minimum quadopt=(dt=66.3358,rms=0.419519) vs oldopt=(dt=32,rms=0.420377)
#GCMRL# 533 dt 66.335766 rms 0.420 1.124% neg 0 invalid 762 tFOTS 9.7890 tGradient 7.6910 tsec 18.1330
#FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.418766) vs oldopt=(dt=8,rms=0.418914)
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
#GCMRL# 534 dt 11.200000 rms 0.419 0.000% neg 0 invalid 762 tFOTS 10.0310 tGradient 7.7320 tsec 19.1070
#GCMRL# 535 dt 11.200000 rms 0.419 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7730 tsec 8.4390
#GCMRL# 536 dt 11.200000 rms 0.418 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7850 tsec 8.4370
#GCMRL# 537 dt 11.200000 rms 0.418 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7720 tsec 8.4390
#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.417494) vs oldopt=(dt=32,rms=0.417535)
#GCMRL# 538 dt 44.800000 rms 0.417 0.129% neg 0 invalid 762 tFOTS 9.8740 tGradient 7.7610 tsec 18.2960
#FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.417241) vs oldopt=(dt=8,rms=0.417279)
setting smoothness cost coefficient to 0.400
#GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.423798
#FOTS# QuadFit found better minimum quadopt=(dt=2.304,rms=0.422956) vs oldopt=(dt=2.88,rms=0.422956)
#GCMRL# 540 dt 2.304000 rms 0.423 0.199% neg 0 invalid 762 tFOTS 9.9590 tGradient 5.3710 tsec 15.9940
#FOTS# QuadFit found better minimum quadopt=(dt=1.008,rms=0.422955) vs oldopt=(dt=0.72,rms=0.422958)
#GCMRL# 541 dt 1.008000 rms 0.423 0.000% neg 0 invalid 762 tFOTS 9.9530 tGradient 5.3840 tsec 16.0200
#GCMRL# 542 dt 1.008000 rms 0.423 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.4360 tsec 6.0980
#GCAMreg# pass 0 level1 2 level2 1 tsec 56.755 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.423656
#FOTS# QuadFit found better minimum quadopt=(dt=8.67257,rms=0.421995) vs oldopt=(dt=11.52,rms=0.422103)
#GCMRL# 544 dt 8.672566 rms 0.422 0.392% neg 0 invalid 762 tFOTS 9.9350 tGradient 5.3290 tsec 15.9310
#FOTS# QuadFit found better minimum quadopt=(dt=13.9429,rms=0.421202) vs oldopt=(dt=11.52,rms=0.421229)
#GCMRL# 545 dt 13.942857 rms 0.421 0.000% neg 0 invalid 762 tFOTS 9.8940 tGradient 5.3130 tsec 15.8870
#GCMRL# 546 dt 13.942857 rms 0.420 0.273% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.2880 tsec 5.9450
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
#GCMRL# 547 dt 13.942857 rms 0.419 0.356% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3220 tsec 6.6340
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
#GCMRL# 548 dt 13.942857 rms 0.417 0.301% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3490 tsec 6.9960
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
#GCMRL# 549 dt 13.942857 rms 0.415 0.468% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3140 tsec 6.9070
iter 0, gcam->neg = 2
after 3 iterations, nbhd size=0, neg = 0
#GCMRL# 550 dt 13.942857 rms 0.413 0.469% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3130 tsec 7.4990
iter 0, gcam->neg = 6
after 9 iterations, nbhd size=1, neg = 0
#GCMRL# 551 dt 13.942857 rms 0.412 0.342% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3090 tsec 9.3160
iter 0, gcam->neg = 3
after 1 iterations, nbhd size=0, neg = 0
#GCMRL# 552 dt 13.942857 rms 0.411 0.129% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3070 tsec 6.9640
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
#GCMRL# 553 dt 13.942857 rms 0.411 -0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.3170 tsec 7.2380
#FOTS# QuadFit found better minimum quadopt=(dt=4.032,rms=0.411389) vs oldopt=(dt=2.88,rms=0.411395)
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
#GCMRL# 554 dt 4.032000 rms 0.411 0.012% neg 0 invalid 762 tFOTS 9.8220 tGradient 5.3100 tsec 16.4260
#FOTS# QuadFit found better minimum quadopt=(dt=0.0016875,rms=0.411365) vs oldopt=(dt=0.0028125,rms=0.411365)
setting smoothness cost coefficient to 1.000
#GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.417255
#GCMRL# 556 dt 0.000000 rms 0.416 0.193% neg 0 invalid 762 tFOTS 9.3460 tGradient 2.1640 tsec 12.1650
#GCAMreg# pass 0 level1 1 level2 1 tsec 36.907 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.417255
#GCMRL# 558 dt 0.000000 rms 0.416 0.193% neg 0 invalid 762 tFOTS 9.3620 tGradient 2.1450 tsec 12.1610
resetting metric properties...
setting smoothness cost coefficient to 2.000
#GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.408762
#FOTS# QuadFit found better minimum quadopt=(dt=1.88843,rms=0.385579) vs oldopt=(dt=1.28,rms=0.388123)
iter 0, gcam->neg = 624
after 13 iterations, nbhd size=1, neg = 0
#GCMRL# 560 dt 1.888427 rms 0.386 5.618% neg 0 invalid 762 tFOTS 9.8500 tGradient 1.6540 tsec 16.6460
#GCMRL# 561 dt 0.000013 rms 0.386 0.000% neg 0 invalid 762 tFOTS 12.4190 tGradient 1.6610 tsec 14.7480
#GCAMreg# pass 0 level1 0 level2 1 tsec 46.245 sigma 0.5
l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.386748
#FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.385744) vs oldopt=(dt=0.02,rms=0.385752)
#GCMRL# 563 dt 0.028000 rms 0.386 0.259% neg 0 invalid 762 tFOTS 9.8530 tGradient 1.6650 tsec 12.1720
#FOTS# QuadFit found better minimum quadopt=(dt=0.007,rms=0.385783) vs oldopt=(dt=0.005,rms=0.385784)
#GCMRL# 564 dt 0.007000 rms 0.386 0.000% neg 0 invalid 762 tFOTS 9.8970 tGradient 1.7050 tsec 12.8720
#GCMRL# 565 dt 0.007000 rms 0.386 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6860 tsec 2.3400
#GCMRL# 566 dt 0.007000 rms 0.386 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.6640 tsec 2.3140
label assignment complete, 0 changed (0.00%)
GCAMregister done in 20.7949 min
Starting GCAMcomputeMaxPriorLabels()
Morphing with label term set to 0 *******************************
Starting GCAMregister()
label assignment complete, 0 changed (0.00%)
npasses = 1, nlevels = 6
#pass# 1 of 1 ************************
enabling zero nodes
setting smoothness cost coefficient to 0.008
#GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.375653
#GCAMreg# pass 0 level1 5 level2 1 tsec 44.041 sigma 0.5
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.375653
#FOTS# QuadFit found better minimum quadopt=(dt=8.092,rms=0.375651) vs oldopt=(dt=5.78,rms=0.375651)
#GCMRL# 569 dt 8.092000 rms 0.376 0.001% neg 0 invalid 762 tFOTS 9.5750 tGradient 21.7470 tsec 31.9640
#FOTS# QuadFit found better minimum quadopt=(dt=2.023,rms=0.375651) vs oldopt=(dt=1.445,rms=0.375651)
#GCMRL# 570 dt 2.023000 rms 0.376 0.000% neg 0 invalid 762 tFOTS 9.5250 tGradient 21.7510 tsec 31.9330
#GCMRL# 571 dt 2.023000 rms 0.376 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 21.7220 tsec 22.3640
setting smoothness cost coefficient to 0.031
#GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.37578
#FOTS# QuadFit found better minimum quadopt=(dt=2.268,rms=0.375776) vs oldopt=(dt=1.62,rms=0.375777)
#GCMRL# 573 dt 2.268000 rms 0.376 0.001% neg 0 invalid 762 tFOTS 9.6600 tGradient 12.4640 tsec 22.7700
#FOTS# QuadFit found better minimum quadopt=(dt=1.944,rms=0.375775) vs oldopt=(dt=1.62,rms=0.375775)
#GCMRL# 574 dt 1.944000 rms 0.376 0.000% neg 0 invalid 762 tFOTS 9.6720 tGradient 12.4470 tsec 22.7840
#GCAMreg# pass 0 level1 4 level2 1 tsec 71.235 sigma 0.5
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.375775
#GCMRL# 576 dt 25.920000 rms 0.376 0.015% neg 0 invalid 762 tFOTS 9.1180 tGradient 12.4730 tsec 22.2380
#FOTS# QuadFit found better minimum quadopt=(dt=20.8,rms=0.375706) vs oldopt=(dt=25.92,rms=0.375708)
#GCMRL# 577 dt 20.800000 rms 0.376 0.000% neg 0 invalid 762 tFOTS 9.6250 tGradient 12.3390 tsec 22.6240
#GCMRL# 578 dt 20.800000 rms 0.376 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.3490 tsec 12.9950
setting smoothness cost coefficient to 0.118
#GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.376188
#FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.375971) vs oldopt=(dt=8,rms=0.375989)
#GCMRL# 580 dt 11.200000 rms 0.376 0.058% neg 0 invalid 762 tFOTS 9.6780 tGradient 7.5370 tsec 17.8630
#FOTS# QuadFit found better minimum quadopt=(dt=6.4,rms=0.37594) vs oldopt=(dt=8,rms=0.375943)
#GCMRL# 581 dt 6.400000 rms 0.376 0.000% neg 0 invalid 762 tFOTS 9.6920 tGradient 7.5480 tsec 17.9080
#GCAMreg# pass 0 level1 3 level2 1 tsec 56.501 sigma 0.5
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.37594
#FOTS# QuadFit found better minimum quadopt=(dt=86.9565,rms=0.374039) vs oldopt=(dt=32,rms=0.374485)
iter 0, gcam->neg = 22
after 9 iterations, nbhd size=1, neg = 0
#GCMRL# 583 dt 86.956522 rms 0.374 0.497% neg 0 invalid 762 tFOTS 10.3890 tGradient 7.5540 tsec 22.0340
#FOTS# QuadFit found better minimum quadopt=(dt=25.4316,rms=0.373277) vs oldopt=(dt=32,rms=0.373375)
iter 0, gcam->neg = 7
after 3 iterations, nbhd size=0, neg = 0
#GCMRL# 584 dt 25.431579 rms 0.373 0.000% neg 0 invalid 762 tFOTS 11.1760 tGradient 7.4570 tsec 20.8760
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
#GCMRL# 585 dt 25.431579 rms 0.373 0.083% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4130 tsec 8.7580
iter 0, gcam->neg = 7
after 2 iterations, nbhd size=0, neg = 0
#GCMRL# 586 dt 25.431579 rms 0.373 0.095% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4340 tsec 9.3730
iter 0, gcam->neg = 9
after 12 iterations, nbhd size=1, neg = 0
#GCMRL# 587 dt 25.431579 rms 0.372 0.083% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.4480 tsec 12.3520
iter 0, gcam->neg = 10
after 5 iterations, nbhd size=0, neg = 0
#GCMRL# 588 dt 25.431579 rms 0.372 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3830 tsec 10.1740
iter 0, gcam->neg = 15
after 11 iterations, nbhd size=1, neg = 0
#GCMRL# 589 dt 25.431579 rms 0.372 0.096% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.3650 tsec 11.9330
#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.371393) vs oldopt=(dt=32,rms=0.371426)
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
setting smoothness cost coefficient to 0.400
#GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.374087
#FOTS# QuadFit found better minimum quadopt=(dt=3.456,rms=0.373984) vs oldopt=(dt=2.88,rms=0.373988)
#GCMRL# 591 dt 3.456000 rms 0.374 0.028% neg 0 invalid 762 tFOTS 11.1670 tGradient 4.9260 tsec 16.8000
#FOTS# QuadFit found better minimum quadopt=(dt=1.008,rms=0.373976) vs oldopt=(dt=0.72,rms=0.373977)
#GCMRL# 592 dt 1.008000 rms 0.374 0.000% neg 0 invalid 762 tFOTS 10.5700 tGradient 4.9290 tsec 16.2250
#GCMRL# 593 dt 1.008000 rms 0.374 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9460 tsec 5.6530
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
#GCAMreg# pass 0 level1 2 level2 1 tsec 58.045 sigma 0.5
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.373974
#FOTS# QuadFit found better minimum quadopt=(dt=21.7358,rms=0.372501) vs oldopt=(dt=11.52,rms=0.372842)
iter 0, gcam->neg = 11
after 3 iterations, nbhd size=0, neg = 0
#GCMRL# 595 dt 21.735849 rms 0.372 0.394% neg 0 invalid 762 tFOTS 11.0670 tGradient 4.9390 tsec 18.2240
#FOTS# QuadFit found better minimum quadopt=(dt=22.8571,rms=0.37164) vs oldopt=(dt=11.52,rms=0.371845)
iter 0, gcam->neg = 17
after 10 iterations, nbhd size=1, neg = 0
#GCMRL# 596 dt 22.857143 rms 0.372 0.000% neg 0 invalid 762 tFOTS 11.0920 tGradient 4.8960 tsec 20.3040
iter 0, gcam->neg = 27
after 15 iterations, nbhd size=1, neg = 0
setting smoothness cost coefficient to 1.000
#GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.376315
#FOTS# QuadFit found better minimum quadopt=(dt=-0.000160217,rms=0.376315) vs oldopt=(dt=7.8125e-05,rms=0.376315)
#GCMRL# 598 dt -0.000160 rms 0.376 0.000% neg 0 invalid 762 tFOTS 14.0700 tGradient 1.7780 tsec 16.5590
#GCAMreg# pass 0 level1 1 level2 1 tsec 42.378 sigma 0.5
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.376315
resetting metric properties...
setting smoothness cost coefficient to 2.000
#GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=2.000...
GCAMRegisterLevel(): init RMS 0.368515
#FOTS# QuadFit found better minimum quadopt=(dt=1.11117,rms=0.361078) vs oldopt=(dt=1.28,rms=0.361224)
iter 0, gcam->neg = 480
after 16 iterations, nbhd size=1, neg = 0
#GCMRL# 601 dt 1.111171 rms 0.362 1.841% neg 0 invalid 762 tFOTS 11.1230 tGradient 1.2830 tsec 18.4880
#FOTS# QuadFit found better minimum quadopt=(dt=2.34375e-05,rms=0.361732) vs oldopt=(dt=1.95313e-05,rms=0.361732)
#GCMRL# 602 dt 0.000023 rms 0.362 0.000% neg 0 invalid 762 tFOTS 12.0890 tGradient 1.2750 tsec 14.0180
#GCAMreg# pass 0 level1 0 level2 1 tsec 46.97 sigma 0.5
l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00
tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes
blurring input image with Gaussian with sigma=0.500...
GCAMRegisterLevel(): init RMS 0.361732
#FOTS# QuadFit found better minimum quadopt=(dt=0.064,rms=0.361659) vs oldopt=(dt=0.08,rms=0.361659)
#GCMRL# 604 dt 0.064000 rms 0.362 0.020% neg 0 invalid 762 tFOTS 9.6420 tGradient 1.2720 tsec 11.5550
#FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.361639) vs oldopt=(dt=0.02,rms=0.361643)
#GCMRL# 605 dt 0.028000 rms 0.362 0.000% neg 0 invalid 762 tFOTS 9.6250 tGradient 1.2740 tsec 11.5530
#GCMRL# 606 dt 0.028000 rms 0.362 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 1.2720 tsec 1.9100
GCAMregister done in 11.9923 min
writing output transformation to transforms/talairach.m3z...
GCAMwrite
Calls to gcamLogLikelihoodEnergy 4499 tmin = 7.82202
Calls to gcamLabelEnergy 3971 tmin = 0.759183
Calls to gcamJacobianEnergy 4499 tmin = 10.9935
Calls to gcamSmoothnessEnergy 4499 tmin = 8.6203
Calls to gcamLogLikelihoodTerm 608 tmin = 2.62498
Calls to gcamLabelTerm 568 tmin = 4.20548
Calls to gcamJacobianTerm 608 tmin = 7.31055
Calls to gcamSmoothnessTerm 608 tmin = 2.11878
Calls to gcamComputeGradient 608 tmin = 125.319
Calls to gcamComputeMetricProperties 6257 tmin = 10.4899
mri_ca_register took 2 hours, 54 minutes and 48 seconds.
#VMPC# mri_ca_register VmPeak 2023724
FSRUNTIME@ mri_ca_register 2.9135 hours 1 threads
#--------------------------------------
#@# SubCort Seg Fri Jun 13 00:27:47 UTC 2025
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer-7.3.2/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz
sysname Linux
hostname fv-az1121-699
machine x86_64
setenv SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer-7.3.2/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz
relabeling unlikely voxels with window_size = 9 and prior threshold 0.30
using Gibbs prior factor = 0.500
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-renormalize_mean 0.500
-regularize 0.500
== Number of threads available to for OpenMP = 1 ==
reading 1 input volumes
reading classifier array from /opt/freesurfer-7.3.2/average/RB_all_2020-01-02.gca
reading input volume from norm.mgz
average std[0] = 7.2
reading transform from transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 6.27
Atlas used for the 3D morph was /opt/freesurfer-7.3.2/average/RB_all_2020-01-02.gca
average std = 7.2 using min determinant for regularization = 5.2
0 singular and 0 ill-conditioned covariance matrices regularized
labeling volume...
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.15521 (20)
mri peak = 0.17945 ( 7)
Left_Lateral_Ventricle (4): linear fit = 0.35 x + 0.0 (1560 voxels, overlap=0.004)
Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1560 voxels, peak = 7), gca=8.0
gca peak = 0.20380 (13)
mri peak = 0.17272 ( 7)
Right_Lateral_Ventricle (43): linear fit = 0.43 x + 0.0 (1589 voxels, overlap=0.049)
Right_Lateral_Ventricle (43): linear fit = 0.43 x + 0.0 (1589 voxels, peak = 6), gca=5.5
gca peak = 0.26283 (96)
mri peak = 0.16332 (106)
Right_Pallidum (52): linear fit = 1.10 x + 0.0 (819 voxels, overlap=0.128)
Right_Pallidum (52): linear fit = 1.10 x + 0.0 (819 voxels, peak = 105), gca=105.1
gca peak = 0.15814 (97)
mri peak = 0.11072 (106)
Left_Pallidum (13): linear fit = 1.12 x + 0.0 (858 voxels, overlap=0.026)
Left_Pallidum (13): linear fit = 1.12 x + 0.0 (858 voxels, peak = 109), gca=109.1
gca peak = 0.27624 (56)
mri peak = 0.10696 (56)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (782 voxels, overlap=1.011)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (782 voxels, peak = 56), gca=56.0
gca peak = 0.28723 (59)
mri peak = 0.09347 (60)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (838 voxels, overlap=1.011)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (838 voxels, peak = 60), gca=60.5
gca peak = 0.07623 (103)
mri peak = 0.13857 (102)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41973 voxels, overlap=0.615)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41973 voxels, peak = 103), gca=103.0
gca peak = 0.07837 (105)
mri peak = 0.13751 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (43265 voxels, overlap=0.620)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (43265 voxels, peak = 105), gca=105.0
gca peak = 0.10165 (58)
mri peak = 0.04398 (66)
Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (29448 voxels, overlap=0.783)
Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (29448 voxels, peak = 64), gca=63.5
gca peak = 0.11113 (58)
mri peak = 0.04406 (64)
Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (28388 voxels, overlap=0.735)
Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (28388 voxels, peak = 62), gca=62.4
gca peak = 0.27796 (67)
mri peak = 0.18231 (76)
Right_Caudate (50): linear fit = 1.12 x + 0.0 (935 voxels, overlap=0.231)
Right_Caudate (50): linear fit = 1.12 x + 0.0 (935 voxels, peak = 75), gca=74.7
gca peak = 0.14473 (69)
mri peak = 0.13884 (77)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (901 voxels, overlap=0.937)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (901 voxels, peak = 69), gca=69.0
gca peak = 0.14301 (56)
mri peak = 0.05310 (48)
Left_Cerebellum_Cortex (8): linear fit = 0.86 x + 0.0 (14929 voxels, overlap=0.755)
Left_Cerebellum_Cortex (8): linear fit = 0.86 x + 0.0 (14929 voxels, peak = 48), gca=47.9
gca peak = 0.14610 (55)
mri peak = 0.04965 (46)
Right_Cerebellum_Cortex (47): linear fit = 0.83 x + 0.0 (15407 voxels, overlap=0.643)
Right_Cerebellum_Cortex (47): linear fit = 0.83 x + 0.0 (15407 voxels, peak = 46), gca=45.9
gca peak = 0.16309 (85)
mri peak = 0.07994 (89)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5075 voxels, overlap=0.821)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5075 voxels, peak = 91), gca=90.5
gca peak = 0.15172 (84)
mri peak = 0.08530 (88)
Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5192 voxels, overlap=0.827)
Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5192 voxels, peak = 89), gca=89.5
gca peak = 0.30461 (58)
mri peak = 0.10000 (63)
Left_Amygdala (18): linear fit = 1.10 x + 0.0 (469 voxels, overlap=0.856)
Left_Amygdala (18): linear fit = 1.10 x + 0.0 (469 voxels, peak = 64), gca=63.5
gca peak = 0.32293 (57)
mri peak = 0.11073 (62)
Right_Amygdala (54): linear fit = 1.10 x + 0.0 (449 voxels, overlap=0.625)
Right_Amygdala (54): linear fit = 1.10 x + 0.0 (449 voxels, peak = 62), gca=62.4
gca peak = 0.11083 (90)
mri peak = 0.08778 (91)
Left_Thalamus (10): linear fit = 1.05 x + 0.0 (4105 voxels, overlap=0.842)
Left_Thalamus (10): linear fit = 1.05 x + 0.0 (4105 voxels, peak = 95), gca=94.9
gca peak = 0.11393 (83)
mri peak = 0.08291 (89)
Right_Thalamus (49): linear fit = 1.10 x + 0.0 (4093 voxels, overlap=0.697)
Right_Thalamus (49): linear fit = 1.10 x + 0.0 (4093 voxels, peak = 91), gca=90.9
gca peak = 0.08575 (81)
mri peak = 0.09072 (84)
Left_Putamen (12): linear fit = 1.10 x + 0.0 (1968 voxels, overlap=0.477)
Left_Putamen (12): linear fit = 1.10 x + 0.0 (1968 voxels, peak = 89), gca=88.7
gca peak = 0.08618 (78)
mri peak = 0.09372 (88)
Right_Putamen (51): linear fit = 1.10 x + 0.0 (2102 voxels, overlap=0.522)
Right_Putamen (51): linear fit = 1.10 x + 0.0 (2102 voxels, peak = 85), gca=85.4
gca peak = 0.08005 (78)
mri peak = 0.06509 (96)
Brain_Stem (16): linear fit = 1.18 x + 0.0 (10329 voxels, overlap=0.363)
Brain_Stem (16): linear fit = 1.18 x + 0.0 (10329 voxels, peak = 92), gca=92.4
gca peak = 0.12854 (88)
mri peak = 0.08940 (101)
Right_VentralDC (60): linear fit = 1.20 x + 0.0 (1512 voxels, overlap=0.017)
Right_VentralDC (60): linear fit = 1.20 x + 0.0 (1512 voxels, peak = 105), gca=105.2
gca peak = 0.15703 (87)
mri peak = 0.10143 (101)
Left_VentralDC (28): linear fit = 1.20 x + 0.0 (1493 voxels, overlap=0.012)
Left_VentralDC (28): linear fit = 1.20 x + 0.0 (1493 voxels, peak = 104), gca=104.0
gca peak = 0.17522 (25)
mri peak = 0.42105 ( 9)
gca peak = 0.17113 (14)
mri peak = 0.35667 ( 3)
Fourth_Ventricle (15): linear fit = 0.12 x + 0.0 (291 voxels, overlap=0.016)
Fourth_Ventricle (15): linear fit = 0.12 x + 0.0 (291 voxels, peak = 2), gca=1.8
gca peak Unknown = 0.94777 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16627 (28)
gca peak Third_Ventricle = 0.17522 (25)
gca peak Fourth_Ventricle = 0.17113 (14)
gca peak CSF = 0.20346 (36)
gca peak Left_Accumbens_area = 0.70646 (62)
gca peak Left_undetermined = 1.00000 (28)
gca peak Left_vessel = 0.89917 (53)
gca peak Left_choroid_plexus = 0.11689 (35)
gca peak Right_Inf_Lat_Vent = 0.25504 (23)
gca peak Right_Accumbens_area = 0.31650 (65)
gca peak Right_vessel = 0.77268 (52)
gca peak Right_choroid_plexus = 0.13275 (38)
gca peak Fifth_Ventricle = 0.60973 (33)
gca peak WM_hypointensities = 0.11013 (77)
gca peak non_WM_hypointensities = 0.11354 (41)
gca peak Optic_Chiasm = 0.51646 (76)
not using caudate to estimate GM means
estimating mean gm scale to be 1.06 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 0.41 x + 0.0
Left_Pallidum too bright - rescaling by 0.924 (from 1.125) to 100.9 (was 109.1)
Right_Pallidum too bright - rescaling by 0.960 (from 1.095) to 100.9 (was 105.1)
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.31706 ( 7)
mri peak = 0.17945 ( 7)
Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (1560 voxels, overlap=0.926)
Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (1560 voxels, peak = 6), gca=5.8
gca peak = 0.29738 ( 6)
mri peak = 0.17272 ( 7)
Right_Lateral_Ventricle (43): linear fit = 1.25 x + 0.0 (1589 voxels, overlap=0.924)
Right_Lateral_Ventricle (43): linear fit = 1.25 x + 0.0 (1589 voxels, peak = 7), gca=7.5
gca peak = 0.28156 (100)
mri peak = 0.16332 (106)
Right_Pallidum (52): linear fit = 1.04 x + 0.0 (819 voxels, overlap=0.821)
Right_Pallidum (52): linear fit = 1.04 x + 0.0 (819 voxels, peak = 104), gca=104.5
gca peak = 0.15478 (99)
mri peak = 0.11072 (106)
Left_Pallidum (13): linear fit = 1.08 x + 0.0 (858 voxels, overlap=0.466)
Left_Pallidum (13): linear fit = 1.08 x + 0.0 (858 voxels, peak = 106), gca=106.4
gca peak = 0.26416 (56)
mri peak = 0.10696 (56)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (782 voxels, overlap=1.011)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (782 voxels, peak = 56), gca=56.0
gca peak = 0.33569 (58)
mri peak = 0.09347 (60)
Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (838 voxels, overlap=1.009)
Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (838 voxels, peak = 57), gca=57.1
gca peak = 0.07621 (103)
mri peak = 0.13857 (102)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41973 voxels, overlap=0.615)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41973 voxels, peak = 103), gca=103.0
gca peak = 0.07845 (105)
mri peak = 0.13751 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (43265 voxels, overlap=0.620)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (43265 voxels, peak = 105), gca=105.0
gca peak = 0.08782 (63)
mri peak = 0.04398 (66)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (29448 voxels, overlap=0.960)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (29448 voxels, peak = 63), gca=63.0
gca peak = 0.10681 (63)
mri peak = 0.04406 (64)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (28388 voxels, overlap=0.926)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (28388 voxels, peak = 65), gca=64.6
gca peak = 0.22478 (74)
mri peak = 0.18231 (76)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (935 voxels, overlap=1.000)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (935 voxels, peak = 74), gca=74.0
gca peak = 0.14473 (69)
mri peak = 0.13884 (77)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (901 voxels, overlap=0.937)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (901 voxels, peak = 69), gca=69.0
gca peak = 0.16470 (48)
mri peak = 0.05310 (48)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (14929 voxels, overlap=1.000)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (14929 voxels, peak = 48), gca=48.0
gca peak = 0.18229 (46)
mri peak = 0.04965 (46)
Right_Cerebellum_Cortex (47): linear fit = 1.05 x + 0.0 (15407 voxels, overlap=0.996)
Right_Cerebellum_Cortex (47): linear fit = 1.05 x + 0.0 (15407 voxels, peak = 49), gca=48.5
gca peak = 0.15119 (90)
mri peak = 0.07994 (89)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5075 voxels, overlap=0.982)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5075 voxels, peak = 90), gca=89.6
gca peak = 0.16700 (90)
mri peak = 0.08530 (88)
Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5192 voxels, overlap=0.982)
Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5192 voxels, peak = 89), gca=88.7
gca peak = 0.23301 (63)
mri peak = 0.10000 (63)
Left_Amygdala (18): linear fit = 1.01 x + 0.0 (469 voxels, overlap=1.028)
Left_Amygdala (18): linear fit = 1.01 x + 0.0 (469 voxels, peak = 64), gca=63.9
gca peak = 0.29567 (63)
mri peak = 0.11073 (62)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (449 voxels, overlap=1.021)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (449 voxels, peak = 63), gca=63.0
gca peak = 0.10834 (95)
mri peak = 0.08778 (91)
Left_Thalamus (10): linear fit = 0.99 x + 0.0 (4105 voxels, overlap=0.971)
Left_Thalamus (10): linear fit = 0.99 x + 0.0 (4105 voxels, peak = 94), gca=93.6
gca peak = 0.11610 (91)
mri peak = 0.08291 (89)
Right_Thalamus (49): linear fit = 1.00 x + 0.0 (4093 voxels, overlap=0.955)
Right_Thalamus (49): linear fit = 1.00 x + 0.0 (4093 voxels, peak = 91), gca=91.0
gca peak = 0.07778 (89)
mri peak = 0.09072 (84)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1968 voxels, overlap=0.718)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1968 voxels, peak = 89), gca=89.0
gca peak = 0.08743 (83)
mri peak = 0.09372 (88)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2102 voxels, overlap=0.840)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2102 voxels, peak = 83), gca=83.0
gca peak = 0.07618 (93)
mri peak = 0.06509 (96)
Brain_Stem (16): linear fit = 0.98 x + 0.0 (10329 voxels, overlap=0.855)
Brain_Stem (16): linear fit = 0.98 x + 0.0 (10329 voxels, peak = 91), gca=90.7
gca peak = 0.10886 (105)
mri peak = 0.08940 (101)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1512 voxels, overlap=0.835)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1512 voxels, peak = 106), gca=105.5
gca peak = 0.16520 (102)
mri peak = 0.10143 (101)
Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1493 voxels, overlap=0.880)
Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1493 voxels, peak = 100), gca=100.5
gca peak = 0.33670 (11)
mri peak = 0.42105 ( 9)
gca peak = 0.38155 ( 6)
mri peak = 0.35667 ( 3)
Fourth_Ventricle (15): linear fit = 0.32 x + 0.0 (291 voxels, overlap=0.435)
Fourth_Ventricle (15): linear fit = 0.32 x + 0.0 (291 voxels, peak = 2), gca=1.9
gca peak Unknown = 0.94777 ( 0)
gca peak Left_Inf_Lat_Vent = 0.20560 (29)
gca peak Third_Ventricle = 0.33670 (11)
gca peak Fourth_Ventricle = 0.38155 ( 6)
gca peak CSF = 0.34330 (15)
gca peak Left_Accumbens_area = 0.61521 (62)
gca peak Left_undetermined = 1.00000 (28)
gca peak Left_vessel = 0.89917 (53)
gca peak Left_choroid_plexus = 0.11689 (35)
gca peak Right_Inf_Lat_Vent = 0.25695 (23)
gca peak Right_Accumbens_area = 0.37254 (72)
gca peak Right_vessel = 0.77268 (52)
gca peak Right_choroid_plexus = 0.13275 (38)
gca peak Fifth_Ventricle = 0.59846 (14)
gca peak WM_hypointensities = 0.11042 (77)
gca peak non_WM_hypointensities = 0.11354 (41)
gca peak Optic_Chiasm = 0.54524 (76)
not using caudate to estimate GM means
estimating mean gm scale to be 1.00 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.03 x + 0.0
Left_Pallidum too bright - rescaling by 0.948 (from 1.075) to 100.9 (was 106.4)
Right_Pallidum too bright - rescaling by 0.965 (from 1.045) to 100.9 (was 104.5)
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt
47186 voxels changed in iteration 0 of unlikely voxel relabeling
187 voxels changed in iteration 1 of unlikely voxel relabeling
4 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
27342 gm and wm labels changed (%33 to gray, %67 to white out of all changed labels)
283 hippocampal voxels changed.
0 amygdala voxels changed.
Reclassifying using Gibbs Priors
pass 1: 60355 changed. image ll: -2.078, PF=0.500
pass 2: 16145 changed. image ll: -2.078, PF=0.500
pass 3: 5268 changed.
pass 4: 1940 changed.
35968 voxels changed in iteration 0 of unlikely voxel relabeling
451 voxels changed in iteration 1 of unlikely voxel relabeling
81 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
5829 voxels changed in iteration 0 of unlikely voxel relabeling
91 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 of unlikely voxel relabeling
4774 voxels changed in iteration 0 of unlikely voxel relabeling
31 voxels changed in iteration 1 of unlikely voxel relabeling
2 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
4560 voxels changed in iteration 0 of unlikely voxel relabeling
29 voxels changed in iteration 1 of unlikely voxel relabeling
2 voxels changed in iteration 2 of unlikely voxel relabeling
1 voxels changed in iteration 3 of unlikely voxel relabeling
0 voxels changed in iteration 4 of unlikely voxel relabeling
!!!!!!!!! ventricle segment 1 with volume 7087 above threshold 100 - not erasing !!!!!!!!!!
!!!!!!!!! ventricle segment 0 with volume 561 above threshold 100 - not erasing !!!!!!!!!!
!!!!!!!!! ventricle segment 1 with volume 7108 above threshold 100 - not erasing !!!!!!!!!!
!!!!!!!!! ventricle segment 0 with volume 504 above threshold 100 - not erasing !!!!!!!!!!
writing labeled volume to aseg.auto_noCCseg.mgz
mri_ca_label utimesec 1423.350186
mri_ca_label stimesec 1.089969
mri_ca_label ru_maxrss 2107680
mri_ca_label ru_ixrss 0
mri_ca_label ru_idrss 0
mri_ca_label ru_isrss 0
mri_ca_label ru_minflt 426963
mri_ca_label ru_majflt 162
mri_ca_label ru_nswap 0
mri_ca_label ru_inblock 0
mri_ca_label ru_oublock 672
mri_ca_label ru_msgsnd 0
mri_ca_label ru_msgrcv 0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw 498
mri_ca_label ru_nivcsw 5594
auto-labeling took 23 minutes and 45 seconds.
#--------------------------------------
#@# CC Seg Fri Jun 13 00:51:31 UTC 2025
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /tmp/tmps594ishs/freesurfer_output/subjectname/mri/transforms/cc_up.lta subjectname
will read input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
will write lta as /tmp/tmps594ishs/freesurfer_output/subjectname/mri/transforms/cc_up.lta
reading aseg from /tmp/tmps594ishs/freesurfer_output/subjectname/mri/aseg.auto_noCCseg.mgz
reading norm from /tmp/tmps594ishs/freesurfer_output/subjectname/mri/norm.mgz
17460 voxels in left wm, 19637 in right wm, xrange [126, 131]
searching rotation angles z=[-7 7], y=[-7 7]
searching scale 1 Z rot -7.0
searching scale 1 Z rot -6.7
searching scale 1 Z rot -6.2
searching scale 1 Z rot -5.7
searching scale 1 Z rot -5.2
searching scale 1 Z rot -5.0
searching scale 1 Z rot -4.5
searching scale 1 Z rot -4.0
searching scale 1 Z rot -3.5
searching scale 1 Z rot -3.2
searching scale 1 Z rot -2.7
searching scale 1 Z rot -2.2
searching scale 1 Z rot -2.0
searching scale 1 Z rot -1.5
searching scale 1 Z rot -1.0
searching scale 1 Z rot -0.5
searching scale 1 Z rot -0.2
searching scale 1 Z rot 0.3
searching scale 1 Z rot 0.8
searching scale 1 Z rot 1.3
searching scale 1 Z rot 1.5
searching scale 1 Z rot 2.0
searching scale 1 Z rot 2.5
searching scale 1 Z rot 3.0
searching scale 1 Z rot 3.3
searching scale 1 Z rot 3.8
searching scale 1 Z rot 4.3
searching scale 1 Z rot 4.8
searching scale 1 Z rot 5.0
searching scale 1 Z rot 5.5
searching scale 1 Z rot 6.0
searching scale 1 Z rot 6.5
searching scale 1 Z rot 6.8
global minimum found at slice 128.0, rotations (-0.13, 0.03)
final transformation (x=128.0, yr=-0.129, zr=0.034):
1.00000 -0.00059 -0.00224 0.20948;
0.00059 1.00000 -0.00000 35.92439;
0.00224 0.00000 1.00000 36.71302;
0.00000 0.00000 0.00000 1.00000;
updating x range to be [127, 131] in xformed coordinates
best xformed slice 128
min_x_fornix = 150
min_x_fornix = 156
min_x_fornix = 158
min_x_fornix = 156
min_x_fornix = 152
cc center is found at 128 92 91
eigenvectors:
-0.00013 -0.00000 1.00000;
-0.16866 -0.98567 -0.00002;
0.98567 -0.16866 0.00012;
error in mid anterior detected - correcting...
writing aseg with callosum to /tmp/tmps594ishs/freesurfer_output/subjectname/mri/aseg.auto.mgz...
corpus callosum segmentation took 0.3 minutes
#VMPC# mri_cc VmPeak 450068
mri_cc done
#--------------------------------------
#@# Merge ASeg Fri Jun 13 00:51:51 UTC 2025
cp aseg.auto.mgz aseg.presurf.mgz
#--------------------------------------------
#@# Intensity Normalization2 Fri Jun 13 00:51:51 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/mri
mri_normalize -seed 1234 -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz
setting seed for random number genererator to 1234
assuming input volume is MGH (Van der Kouwe) MP-RAGE
using segmentation for initial intensity normalization
using MR volume brainmask.mgz to mask input volume...
reading mri_src from norm.mgz...
Reading aseg aseg.presurf.mgz
normalizing image...
NOT doing gentle normalization with control points/label
processing with aseg
removing outliers in the aseg WM...
308 control points removed
Building bias image
building Voronoi diagram...
performing soap bubble smoothing, sigma = 0...
Smoothing with sigma 8
Applying bias correction
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 63 (63), valley at 29 (29)
csf peak at 32, setting threshold to 52
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 64 (64), valley at 25 (25)
csf peak at 33, setting threshold to 53
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 2 minutes and 3 seconds.
#--------------------------------------------
#@# Mask BFS Fri Jun 13 00:53:56 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5
DoAbs = 0
Found 1563568 voxels in mask (pct= 9.32)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Fri Jun 13 00:53:57 UTC 2025
AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz
mri_segment -wsizemm 13 -mprage antsdn.brain.mgz wm.seg.mgz
wsizemm = 13, voxres = 1, wsize = 13
Widening wm low from 89 to 79
assuming input volume is MGH (Van der Kouwe) MP-RAGE
wm mean: 110
wsize: 13
wm low: 79
wm hi: 125
gray low: 30
gray hi: 99
Doing initial trinary intensity segmentation
Using local statistics to label ambiguous voxels
Autodetecting stats
Computing class statistics for intensity windows...
CCS WM (103.0): 102.6 +- 6.3 [79.0 --> 125.0]
CCS GM (74.0) : 72.3 +- 10.5 [30.0 --> 95.0]
white_mean 102.629
white_sigma 6.3106
gray_mean 72.3238
gray_sigma 10.4832
setting bottom of white matter range wm_low to 82.8
setting top of gray matter range gray_hi to 93.3
wm_low 82.807
wm_hi 125
gray_low 30
gray_hi 93.2901
Redoing initial intensity segmentation...
Recomputing local statistics to label ambiguous voxels...
wm_low 82.807
wm_hi 125
gray_low 30
gray_hi 93.2901
using local geometry to label remaining ambiguous voxels...
polvwsize = 5, polvlen = 3, gray_hi = 93.2901, wm_low = 82.807
MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=93.2901, wmlow=82.807
116645 voxels processed (0.70%)
54510 voxels white (0.32%)
62135 voxels non-white (0.37%)
Reclassifying voxels using Gaussian border classifier niter=1
MRIreclassify(): wm_low=77.807, gray_hi=93.2901, wsize=13
207002 voxels tested (1.23%)
40536 voxels changed (0.24%)
41711 multi-scale searches (0.25%)
Recovering bright white
MRIrecoverBrightWhite()
wm_low 82.807
wm_hi 125
slack 6.3106
pct_thresh 0.33
intensity_thresh 131.311
nvox_thresh 8.58
181 voxels tested (0.00%)
37 voxels changed (0.00%)
removing voxels with positive offset direction...
MRIremoveWrongDirection() wsize=3, lowthr=77.807, hithr=93.2901
smoothing input volume with sigma = 0.250
78157 voxels tested (0.47%)
14991 voxels changed (0.09%)
thicken = 1
removing 1-dimensional structures...
MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5
2692 sparsely connected voxels removed in 1 iterations
thickening thin strands....
thickness 4
nsegments 20
wm_hi 125
948 diagonally connected voxels added...
MRIthickenThinWMStrands(): thickness=4, nsegments=20
20 segments, 4508 filled
MRIfindBrightNonWM(): 1452 bright non-wm voxels segmented.
MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230
white matter segmentation took 0.9 minutes
writing output to wm.seg.mgz...
mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz
preserving editing changes in input volume...
auto filling took 0.40 minutes
reading wm segmentation from wm.seg.mgz...
0 voxels added to wm to prevent paths from MTL structures to cortex
2913 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 44278 voxels turned on, 31168 voxels turned off.
propagating editing to output volume from wm.seg.mgz
writing edited volume to wm.asegedit.mgz....
mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
Iteration Number : 1
pass 1 (xy+): 10 found - 10 modified | TOTAL: 10
pass 2 (xy+): 0 found - 10 modified | TOTAL: 10
pass 1 (xy-): 9 found - 9 modified | TOTAL: 19
pass 2 (xy-): 0 found - 9 modified | TOTAL: 19
pass 1 (yz+): 18 found - 18 modified | TOTAL: 37
pass 2 (yz+): 0 found - 18 modified | TOTAL: 37
pass 1 (yz-): 19 found - 19 modified | TOTAL: 56
pass 2 (yz-): 0 found - 19 modified | TOTAL: 56
pass 1 (xz+): 17 found - 17 modified | TOTAL: 73
pass 2 (xz+): 0 found - 17 modified | TOTAL: 73
pass 1 (xz-): 9 found - 9 modified | TOTAL: 82
pass 2 (xz-): 0 found - 9 modified | TOTAL: 82
Iteration Number : 1
pass 1 (+++): 12 found - 12 modified | TOTAL: 12
pass 2 (+++): 0 found - 12 modified | TOTAL: 12
pass 1 (+++): 12 found - 12 modified | TOTAL: 24
pass 2 (+++): 0 found - 12 modified | TOTAL: 24
pass 1 (+++): 16 found - 16 modified | TOTAL: 40
pass 2 (+++): 0 found - 16 modified | TOTAL: 40
pass 1 (+++): 3 found - 3 modified | TOTAL: 43
pass 2 (+++): 0 found - 3 modified | TOTAL: 43
Iteration Number : 1
pass 1 (++): 43 found - 43 modified | TOTAL: 43
pass 2 (++): 0 found - 43 modified | TOTAL: 43
pass 1 (+-): 18 found - 18 modified | TOTAL: 61
pass 2 (+-): 0 found - 18 modified | TOTAL: 61
pass 1 (--): 44 found - 44 modified | TOTAL: 105
pass 2 (--): 0 found - 44 modified | TOTAL: 105
pass 1 (-+): 15 found - 15 modified | TOTAL: 120
pass 2 (-+): 0 found - 15 modified | TOTAL: 120
Iteration Number : 2
pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
pass 1 (xy-): 1 found - 1 modified | TOTAL: 1
pass 2 (xy-): 0 found - 1 modified | TOTAL: 1
pass 1 (yz+): 6 found - 6 modified | TOTAL: 7
pass 2 (yz+): 0 found - 6 modified | TOTAL: 7
pass 1 (yz-): 0 found - 0 modified | TOTAL: 7
pass 1 (xz+): 0 found - 0 modified | TOTAL: 7
pass 1 (xz-): 2 found - 2 modified | TOTAL: 9
pass 2 (xz-): 0 found - 2 modified | TOTAL: 9
Iteration Number : 2
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 2
pass 1 (++): 0 found - 0 modified | TOTAL: 0
pass 1 (+-): 1 found - 1 modified | TOTAL: 1
pass 2 (+-): 0 found - 1 modified | TOTAL: 1
pass 1 (--): 1 found - 1 modified | TOTAL: 2
pass 2 (--): 0 found - 1 modified | TOTAL: 2
pass 1 (-+): 3 found - 3 modified | TOTAL: 5
pass 2 (-+): 0 found - 3 modified | TOTAL: 5
Iteration Number : 3
pass 1 (xy+): 1 found - 1 modified | TOTAL: 1
pass 2 (xy+): 0 found - 1 modified | TOTAL: 1
pass 1 (xy-): 0 found - 0 modified | TOTAL: 1
pass 1 (yz+): 0 found - 0 modified | TOTAL: 1
pass 1 (yz-): 0 found - 0 modified | TOTAL: 1
pass 1 (xz+): 0 found - 0 modified | TOTAL: 1
pass 1 (xz-): 0 found - 0 modified | TOTAL: 1
Iteration Number : 3
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 3
pass 1 (++): 0 found - 0 modified | TOTAL: 0
pass 1 (+-): 0 found - 0 modified | TOTAL: 0
pass 1 (--): 0 found - 0 modified | TOTAL: 0
pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Iteration Number : 4
pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
Iteration Number : 4
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 4
pass 1 (++): 0 found - 0 modified | TOTAL: 0
pass 1 (+-): 0 found - 0 modified | TOTAL: 0
pass 1 (--): 0 found - 0 modified | TOTAL: 0
pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Total Number of Modified Voxels = 260 (out of 560962: 0.046349)
binarizing input wm segmentation...
Ambiguous edge configurations...
mri_pretess done
#--------------------------------------------
#@# Fill Fri Jun 13 00:55:49 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/mri
mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz -ctab /opt/freesurfer-7.3.2/SubCorticalMassLUT.txt wm.mgz filled.mgz
logging cutting plane coordinates to ../scripts/ponscc.cut.log...
INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
using segmentation aseg.presurf.mgz...
reading input volume...
done.
searching for cutting planes...voxel to talairach voxel transform
1.05652 -0.00215 0.00803 -9.89665;
0.00000 1.14977 0.30808 -33.66292;
-0.00863 -0.26274 0.98055 28.36463;
0.00000 0.00000 0.00000 1.00000;
voxel to talairach voxel transform
1.05652 -0.00215 0.00803 -9.89665;
0.00000 1.14977 0.30808 -33.66292;
-0.00863 -0.26274 0.98055 28.36463;
0.00000 0.00000 0.00000 1.00000;
reading segmented volume aseg.presurf.mgz
removing CC from segmentation
Looking for area (min, max) = (350, 1400)
area[0] = 1280 (min = 350, max = 1400), aspect = 0.50 (min = 0.10, max = 0.75)
no need to search
using seed (126, 121, 150), TAL = (2.0, 22.0, 7.0)
talairach voxel to voxel transform
0.94644 -0.00000 -0.00775 9.58643;
-0.00208 0.81148 -0.25494 34.52746;
0.00778 0.21743 0.95146 -19.59134;
0.00000 0.00000 0.00000 1.00000;
segmentation indicates cc at (126, 121, 150) --> (2.0, 22.0, 7.0)
done.
filling took 0.7 minutes
talairach cc position changed to (2.00, 22.00, 7.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(20.00, 22.00, 7.00) SRC: (110.64, 94.25, 150.28)
search lh wm seed point around talairach space (-16.00, 22.00, 7.00), SRC: (144.71, 94.17, 150.56)
compute mri_fill using aseg
Erasing Brain Stem and Cerebellum ...
Define left and right masks using aseg:
Building Voronoi diagram ...
Using the Voronoi diagram for separating WM into two hemispheres ...
Find the largest connected component for each hemisphere ...
Embedding colortable
mri_fill done, writing output to filled.mgz...
cp filled.mgz filled.auto.mgz
#--------------------------------------------
#@# Tessellate lh Fri Jun 13 00:56:31 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
Iteration Number : 1
pass 1 (xy+): 1 found - 1 modified | TOTAL: 1
pass 2 (xy+): 0 found - 1 modified | TOTAL: 1
pass 1 (xy-): 0 found - 0 modified | TOTAL: 1
pass 1 (yz+): 16 found - 16 modified | TOTAL: 17
pass 2 (yz+): 0 found - 16 modified | TOTAL: 17
pass 1 (yz-): 9 found - 9 modified | TOTAL: 26
pass 2 (yz-): 0 found - 9 modified | TOTAL: 26
pass 1 (xz+): 1 found - 1 modified | TOTAL: 27
pass 2 (xz+): 0 found - 1 modified | TOTAL: 27
pass 1 (xz-): 0 found - 0 modified | TOTAL: 27
Iteration Number : 1
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 2 found - 2 modified | TOTAL: 2
pass 2 (+++): 0 found - 2 modified | TOTAL: 2
pass 1 (+++): 0 found - 0 modified | TOTAL: 2
Iteration Number : 1
pass 1 (++): 1 found - 1 modified | TOTAL: 1
pass 2 (++): 0 found - 1 modified | TOTAL: 1
pass 1 (+-): 1 found - 1 modified | TOTAL: 2
pass 2 (+-): 0 found - 1 modified | TOTAL: 2
pass 1 (--): 1 found - 1 modified | TOTAL: 3
pass 2 (--): 0 found - 1 modified | TOTAL: 3
pass 1 (-+): 0 found - 0 modified | TOTAL: 3
Iteration Number : 2
pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
pass 1 (xy-): 1 found - 1 modified | TOTAL: 1
pass 2 (xy-): 0 found - 1 modified | TOTAL: 1
pass 1 (yz+): 2 found - 2 modified | TOTAL: 3
pass 2 (yz+): 0 found - 2 modified | TOTAL: 3
pass 1 (yz-): 1 found - 1 modified | TOTAL: 4
pass 2 (yz-): 0 found - 1 modified | TOTAL: 4
pass 1 (xz+): 0 found - 0 modified | TOTAL: 4
pass 1 (xz-): 0 found - 0 modified | TOTAL: 4
Iteration Number : 2
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 2
pass 1 (++): 0 found - 0 modified | TOTAL: 0
pass 1 (+-): 0 found - 0 modified | TOTAL: 0
pass 1 (--): 0 found - 0 modified | TOTAL: 0
pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Iteration Number : 3
pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
Iteration Number : 3
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 3
pass 1 (++): 0 found - 0 modified | TOTAL: 0
pass 1 (+-): 0 found - 0 modified | TOTAL: 0
pass 1 (--): 0 found - 0 modified | TOTAL: 0
pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Total Number of Modified Voxels = 36 (out of 271467: 0.013261)
Ambiguous edge configurations...
mri_pretess done
mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
7.3.2
7.3.2
slice 40: 1563 vertices, 1694 faces
slice 50: 7479 vertices, 7726 faces
slice 60: 16728 vertices, 17090 faces
slice 70: 27379 vertices, 27754 faces
slice 80: 37574 vertices, 37917 faces
slice 90: 47458 vertices, 47807 faces
slice 100: 57721 vertices, 58081 faces
slice 110: 67494 vertices, 67836 faces
slice 120: 76761 vertices, 77125 faces
slice 130: 86317 vertices, 86691 faces
slice 140: 94986 vertices, 95319 faces
slice 150: 102605 vertices, 102883 faces
slice 160: 109181 vertices, 109419 faces
slice 170: 114787 vertices, 114997 faces
slice 180: 119729 vertices, 119898 faces
slice 190: 122912 vertices, 123024 faces
slice 200: 123586 vertices, 123606 faces
slice 210: 123586 vertices, 123606 faces
slice 220: 123586 vertices, 123606 faces
slice 230: 123586 vertices, 123606 faces
slice 240: 123586 vertices, 123606 faces
slice 250: 123586 vertices, 123606 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000 0.00000 0.00000 128.00000;
0.00000 0.00000 1.00000 -128.00000;
0.00000 -1.00000 0.00000 128.00000;
0.00000 0.00000 0.00000 1.00000;
rm -f ../mri/filled-pretess255.mgz
mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix
counting number of connected components...
123586 voxel in cpt #1: X=-20 [v=123586,e=370818,f=247212] located at (-27.235659, -22.251646, 30.684002)
For the whole surface: X=-20 [v=123586,e=370818,f=247212]
One single component has been found
nothing to do
done
#--------------------------------------------
#@# Tessellate rh Fri Jun 13 00:56:35 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
Iteration Number : 1
pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
pass 1 (xy-): 1 found - 1 modified | TOTAL: 1
pass 2 (xy-): 0 found - 1 modified | TOTAL: 1
pass 1 (yz+): 9 found - 9 modified | TOTAL: 10
pass 2 (yz+): 0 found - 9 modified | TOTAL: 10
pass 1 (yz-): 16 found - 16 modified | TOTAL: 26
pass 2 (yz-): 0 found - 16 modified | TOTAL: 26
pass 1 (xz+): 0 found - 0 modified | TOTAL: 26
pass 1 (xz-): 0 found - 0 modified | TOTAL: 26
Iteration Number : 1
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 1
pass 1 (++): 0 found - 0 modified | TOTAL: 0
pass 1 (+-): 0 found - 0 modified | TOTAL: 0
pass 1 (--): 0 found - 0 modified | TOTAL: 0
pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Iteration Number : 2
pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
Iteration Number : 2
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 2
pass 1 (++): 0 found - 0 modified | TOTAL: 0
pass 1 (+-): 0 found - 0 modified | TOTAL: 0
pass 1 (--): 0 found - 0 modified | TOTAL: 0
pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Total Number of Modified Voxels = 26 (out of 270470: 0.009613)
Ambiguous edge configurations...
mri_pretess done
mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix
7.3.2
7.3.2
slice 40: 1562 vertices, 1687 faces
slice 50: 7406 vertices, 7648 faces
slice 60: 16583 vertices, 16949 faces
slice 70: 27176 vertices, 27548 faces
slice 80: 37330 vertices, 37673 faces
slice 90: 47228 vertices, 47575 faces
slice 100: 57505 vertices, 57869 faces
slice 110: 67438 vertices, 67789 faces
slice 120: 76827 vertices, 77194 faces
slice 130: 86268 vertices, 86647 faces
slice 140: 94765 vertices, 95086 faces
slice 150: 102254 vertices, 102537 faces
slice 160: 108810 vertices, 109053 faces
slice 170: 114390 vertices, 114613 faces
slice 180: 119252 vertices, 119429 faces
slice 190: 122404 vertices, 122520 faces
slice 200: 123084 vertices, 123108 faces
slice 210: 123084 vertices, 123108 faces
slice 220: 123084 vertices, 123108 faces
slice 230: 123084 vertices, 123108 faces
slice 240: 123084 vertices, 123108 faces
slice 250: 123084 vertices, 123108 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000 0.00000 0.00000 128.00000;
0.00000 0.00000 1.00000 -128.00000;
0.00000 -1.00000 0.00000 128.00000;
0.00000 0.00000 0.00000 1.00000;
rm -f ../mri/filled-pretess127.mgz
mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix
counting number of connected components...
123084 voxel in cpt #1: X=-24 [v=123084,e=369324,f=246216] located at (26.963943, -22.324535, 30.661808)
For the whole surface: X=-24 [v=123084,e=369324,f=246216]
One single component has been found
nothing to do
done
#--------------------------------------------
#@# Smooth1 lh Fri Jun 13 00:56:39 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
#--------------------------------------------
#@# Smooth1 rh Fri Jun 13 00:56:41 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
#--------------------------------------------
#@# Inflation1 lh Fri Jun 13 00:56:43 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 47.1 mm, total surface area = 69045 mm^2
step 005: RMS=0.108 (target=0.015)
step 010: RMS=0.080 (target=0.015)
step 015: RMS=0.067 (target=0.015)
step 020: RMS=0.058 (target=0.015)
step 025: RMS=0.051 (target=0.015)
step 030: RMS=0.044 (target=0.015)
step 035: RMS=0.040 (target=0.015)
step 040: RMS=0.037 (target=0.015)
step 045: RMS=0.035 (target=0.015)
step 050: RMS=0.033 (target=0.015)
step 055: RMS=0.032 (target=0.015)
step 060: RMS=0.032 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.2 minutes
inflation complete.
Not saving sulc
mris_inflate utimesec 13.201479
mris_inflate stimesec 0.877965
mris_inflate ru_maxrss 197804
mris_inflate ru_ixrss 0
mris_inflate ru_idrss 0
mris_inflate ru_isrss 0
mris_inflate ru_minflt 424450
mris_inflate ru_majflt 14
mris_inflate ru_nswap 0
mris_inflate ru_inblock 0
mris_inflate ru_oublock 8696
mris_inflate ru_msgsnd 0
mris_inflate ru_msgrcv 0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw 275
mris_inflate ru_nivcsw 125
#--------------------------------------------
#@# Inflation1 rh Fri Jun 13 00:56:57 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 47.0 mm, total surface area = 68801 mm^2
step 005: RMS=0.108 (target=0.015)
step 010: RMS=0.079 (target=0.015)
step 015: RMS=0.067 (target=0.015)
step 020: RMS=0.058 (target=0.015)
step 025: RMS=0.050 (target=0.015)
step 030: RMS=0.043 (target=0.015)
step 035: RMS=0.039 (target=0.015)
step 040: RMS=0.036 (target=0.015)
step 045: RMS=0.034 (target=0.015)
step 050: RMS=0.031 (target=0.015)
step 055: RMS=0.030 (target=0.015)
step 060: RMS=0.029 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.2 minutes
inflation complete.
Not saving sulc
mris_inflate utimesec 12.984337
mris_inflate stimesec 0.845956
mris_inflate ru_maxrss 197436
mris_inflate ru_ixrss 0
mris_inflate ru_idrss 0
mris_inflate ru_isrss 0
mris_inflate ru_minflt 404948
mris_inflate ru_majflt 0
mris_inflate ru_nswap 0
mris_inflate ru_inblock 0
mris_inflate ru_oublock 8664
mris_inflate ru_msgsnd 0
mris_inflate ru_msgrcv 0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw 270
mris_inflate ru_nivcsw 64
#--------------------------------------------
#@# QSphere lh Fri Jun 13 00:57:11 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
doing quick spherical unfolding.
limitting unfolding to 6 passes
using n_averages = 128
setting seed for random number genererator to 1234
version: 7.3.2
available threads: 1
scaling brain by 0.321...
inflating...
projecting onto sphere...
surface projected - minimizing metric distortion...
vertex spacing 1.04 +- 0.60 (0.00-->6.25) (max @ vno 94710 --> 94732)
face area 0.03 +- 0.03 (-0.15-->0.61)
Entering MRISinflateToSphere()
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.279, avgs=0
005/300: dt: 0.9000, rms radial error=176.018, avgs=0
010/300: dt: 0.9000, rms radial error=175.458, avgs=0
015/300: dt: 0.9000, rms radial error=174.720, avgs=0
020/300: dt: 0.9000, rms radial error=173.881, avgs=0
025/300: dt: 0.9000, rms radial error=172.989, avgs=0
030/300: dt: 0.9000, rms radial error=172.071, avgs=0
035/300: dt: 0.9000, rms radial error=171.136, avgs=0
040/300: dt: 0.9000, rms radial error=170.192, avgs=0
045/300: dt: 0.9000, rms radial error=169.246, avgs=0
050/300: dt: 0.9000, rms radial error=168.300, avgs=0
055/300: dt: 0.9000, rms radial error=167.357, avgs=0
060/300: dt: 0.9000, rms radial error=166.417, avgs=0
065/300: dt: 0.9000, rms radial error=165.482, avgs=0
070/300: dt: 0.9000, rms radial error=164.551, avgs=0
075/300: dt: 0.9000, rms radial error=163.625, avgs=0
080/300: dt: 0.9000, rms radial error=162.705, avgs=0
085/300: dt: 0.9000, rms radial error=161.790, avgs=0
090/300: dt: 0.9000, rms radial error=160.880, avgs=0
095/300: dt: 0.9000, rms radial error=159.976, avgs=0
100/300: dt: 0.9000, rms radial error=159.077, avgs=0
105/300: dt: 0.9000, rms radial error=158.183, avgs=0
110/300: dt: 0.9000, rms radial error=157.294, avgs=0
115/300: dt: 0.9000, rms radial error=156.409, avgs=0
120/300: dt: 0.9000, rms radial error=155.530, avgs=0
125/300: dt: 0.9000, rms radial error=154.656, avgs=0
130/300: dt: 0.9000, rms radial error=153.787, avgs=0
135/300: dt: 0.9000, rms radial error=152.923, avgs=0
140/300: dt: 0.9000, rms radial error=152.064, avgs=0
145/300: dt: 0.9000, rms radial error=151.209, avgs=0
150/300: dt: 0.9000, rms radial error=150.359, avgs=0
155/300: dt: 0.9000, rms radial error=149.514, avgs=0
160/300: dt: 0.9000, rms radial error=148.674, avgs=0
165/300: dt: 0.9000, rms radial error=147.838, avgs=0
170/300: dt: 0.9000, rms radial error=147.007, avgs=0
175/300: dt: 0.9000, rms radial error=146.180, avgs=0
180/300: dt: 0.9000, rms radial error=145.358, avgs=0
185/300: dt: 0.9000, rms radial error=144.541, avgs=0
190/300: dt: 0.9000, rms radial error=143.728, avgs=0
195/300: dt: 0.9000, rms radial error=142.920, avgs=0
200/300: dt: 0.9000, rms radial error=142.116, avgs=0
205/300: dt: 0.9000, rms radial error=141.316, avgs=0
210/300: dt: 0.9000, rms radial error=140.521, avgs=0
215/300: dt: 0.9000, rms radial error=139.730, avgs=0
220/300: dt: 0.9000, rms radial error=138.944, avgs=0
225/300: dt: 0.9000, rms radial error=138.162, avgs=0
230/300: dt: 0.9000, rms radial error=137.384, avgs=0
235/300: dt: 0.9000, rms radial error=136.610, avgs=0
240/300: dt: 0.9000, rms radial error=135.841, avgs=0
245/300: dt: 0.9000, rms radial error=135.076, avgs=0
250/300: dt: 0.9000, rms radial error=134.316, avgs=0
255/300: dt: 0.9000, rms radial error=133.559, avgs=0
260/300: dt: 0.9000, rms radial error=132.807, avgs=0
265/300: dt: 0.9000, rms radial error=132.059, avgs=0
270/300: dt: 0.9000, rms radial error=131.315, avgs=0
275/300: dt: 0.9000, rms radial error=130.575, avgs=0
280/300: dt: 0.9000, rms radial error=129.840, avgs=0
285/300: dt: 0.9000, rms radial error=129.108, avgs=0
290/300: dt: 0.9000, rms radial error=128.381, avgs=0
295/300: dt: 0.9000, rms radial error=127.658, avgs=0
300/300: dt: 0.9000, rms radial error=126.939, avgs=0
spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 14165.20
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.01/13 = 0.00042
epoch 2 (K=40.0), pass 1, starting sse = 2219.93
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.01/13 = 0.00043
epoch 3 (K=160.0), pass 1, starting sse = 204.14
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.24/20 = 0.01191
epoch 4 (K=640.0), pass 1, starting sse = 7.62
taking momentum steps...
taking momentum steps...
taki
ng momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.15/24 = 0.00630
final distance error %100000.00
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.0275 hours
FSRUNTIME@ mris_sphere 0.0275 hours 1 threads
#VMPC# mris_sphere VmPeak 473792
mris_sphere done
#--------------------------------------------
#@# QSphere rh Fri Jun 13 00:58:50 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
doing quick spherical unfolding.
limitting unfolding to 6 passes
using n_averages = 128
setting seed for random number genererator to 1234
version: 7.3.2
available threads: 1
scaling brain by 0.321...
inflating...
projecting onto sphere...
surface projected - minimizing metric distortion...
vertex spacing 1.04 +- 0.59 (0.00-->6.15) (max @ vno 56154 --> 56161)
face area 0.03 +- 0.03 (-0.11-->0.63)
Entering MRISinflateToSphere()
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.325, avgs=0
005/300: dt: 0.9000, rms radial error=176.064, avgs=0
010/300: dt: 0.9000, rms radial error=175.503, avgs=0
015/300: dt: 0.9000, rms radial error=174.765, avgs=0
020/300: dt: 0.9000, rms radial error=173.924, avgs=0
025/300: dt: 0.9000, rms radial error=173.023, avgs=0
030/300: dt: 0.9000, rms radial error=172.100, avgs=0
035/300: dt: 0.9000, rms radial error=171.166, avgs=0
040/300: dt: 0.9000, rms radial error=170.223, avgs=0
045/300: dt: 0.9000, rms radial error=169.277, avgs=0
050/300: dt: 0.9000, rms radial error=168.332, avgs=0
055/300: dt: 0.9000, rms radial error=167.390, avgs=0
060/300: dt: 0.9000, rms radial error=166.450, avgs=0
065/300: dt: 0.9000, rms radial error=165.515, avgs=0
070/300: dt: 0.9000, rms radial error=164.584, avgs=0
075/300: dt: 0.9000, rms radial error=163.658, avgs=0
080/300: dt: 0.9000, rms radial error=162.739, avgs=0
085/300: dt: 0.9000, rms radial error=161.825, avgs=0
090/300: dt: 0.9000, rms radial error=160.916, avgs=0
095/300: dt: 0.9000, rms radial error=160.013, avgs=0
100/300: dt: 0.9000, rms radial error=159.115, avgs=0
105/300: dt: 0.9000, rms radial error=158.222, avgs=0
110/300: dt: 0.9000, rms radial error=157.334, avgs=0
115/300: dt: 0.9000, rms radial error=156.451, avgs=0
120/300: dt: 0.9000, rms radial error=155.573, avgs=0
125/300: dt: 0.9000, rms radial error=154.699, avgs=0
130/300: dt: 0.9000, rms radial error=153.830, avgs=0
135/300: dt: 0.9000, rms radial error=152.965, avgs=0
140/300: dt: 0.9000, rms radial error=152.106, avgs=0
145/300: dt: 0.9000, rms radial error=151.251, avgs=0
150/300: dt: 0.9000, rms radial error=150.402, avgs=0
155/300: dt: 0.9000, rms radial error=149.556, avgs=0
160/300: dt: 0.9000, rms radial error=148.716, avgs=0
165/300: dt: 0.9000, rms radial error=147.880, avgs=0
170/300: dt: 0.9000, rms radial error=147.049, avgs=0
175/300: dt: 0.9000, rms radial error=146.223, avgs=0
180/300: dt: 0.9000, rms radial error=145.401, avgs=0
185/300: dt: 0.9000, rms radial error=144.584, avgs=0
190/300: dt: 0.9000, rms radial error=143.771, avgs=0
195/300: dt: 0.9000, rms radial error=142.963, avgs=0
200/300: dt: 0.9000, rms radial error=142.159, avgs=0
205/300: dt: 0.9000, rms radial error=141.359, avgs=0
210/300: dt: 0.9000, rms radial error=140.564, avgs=0
215/300: dt: 0.9000, rms radial error=139.774, avgs=0
220/300: dt: 0.9000, rms radial error=138.987, avgs=0
225/300: dt: 0.9000, rms radial error=138.205, avgs=0
230/300: dt: 0.9000, rms radial error=137.427, avgs=0
235/300: dt: 0.9000, rms radial error=136.654, avgs=0
240/300: dt: 0.9000, rms radial error=135.885, avgs=0
245/300: dt: 0.9000, rms radial error=135.120, avgs=0
250/300: dt: 0.9000, rms radial error=134.359, avgs=0
255/300: dt: 0.9000, rms radial error=133.603, avgs=0
260/300: dt: 0.9000, rms radial error=132.851, avgs=0
265/300: dt: 0.9000, rms radial error=132.103, avgs=0
270/300: dt: 0.9000, rms radial error=131.359, avgs=0
275/300: dt: 0.9000, rms radial error=130.619, avgs=0
280/300: dt: 0.9000, rms radial error=129.884, avgs=0
285/300: dt: 0.9000, rms radial error=129.152, avgs=0
290/300: dt: 0.9000, rms radial error=128.425, avgs=0
295/300: dt: 0.9000, rms radial error=127.701, avgs=0
300/300: dt: 0.9000, rms radial error=126.982, avgs=0
spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 14093.30
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.01/13 = 0.00039
epoch 2 (K=40.0), pass 1, starting sse = 2207.83
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.01/13 = 0.00049
epoch 3 (K=160.0), pass 1, starting sse = 199.57
taking momentum steps...
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.20/18 = 0.01128
epoch 4 (K=640.0), pass 1, starting sse = 7.76
taking momentum steps...
taking momentum steps...
taki
ng momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.20/22 = 0.00914
final distance error %100000.00
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.0263 hours
FSRUNTIME@ mris_sphere 0.0263 hours 1 threads
#VMPC# mris_sphere VmPeak 473028
mris_sphere done
#@# Fix Topology lh Fri Jun 13 01:00:25 UTC 2025
mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 subjectname lh
reading spherical homeomorphism from 'qsphere.nofix'
reading inflated coordinates from 'inflated.nofix'
reading original coordinates from 'orig.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234
*************************************************************
Topology Correction Parameters
retessellation mode: genetic search
number of patches/generation : 10
number of generations : 10
surface mri loglikelihood coefficient : 1.0
volume mri loglikelihood coefficient : 10.0
normal dot loglikelihood coefficient : 1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution : 2
eliminate vertices during search : 1
initial patch selection : 1
select all defect vertices : 0
ordering dependant retessellation: 0
use precomputed edge table : 0
smooth retessellated patch : 2
match retessellated patch : 1
verbose mode : 0
*************************************************************
INFO: assuming .mgz format
writing corrected surface to 'orig.premesh'
7.3.2
7.3.2
before topology correction, eno=-20 (nv=123586, nf=247212, ne=370818, g=11)
using quasi-homeomorphic spherical map to tessellate cortical surface...
Correction of the Topology
Finding true center and radius of Spherical Surface...
done
Surface centered at (0,0,0) with radius 100.0 in 9 iterations
marking ambiguous vertices...
2265 ambiguous faces found in tessellation
segmenting defects...
20 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
20 defects to be corrected
0 vertices coincident
reading input surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Reading original properties of orig.nofix
Reading vertex positions of inflated.nofix
Computing Initial Surface Statistics
-face loglikelihood: -9.3632 (-4.6816)
-vertex loglikelihood: -6.3223 (-3.1612)
-normal dot loglikelihood: -3.6319 (-3.6319)
-quad curv loglikelihood: -6.0087 (-3.0044)
Total Loglikelihood : -25.3261
CORRECTING DEFECT 0 (vertices=64, convex hull=114, v0=46)
After retessellation of defect 0 (v0=46), euler #=-17 (122208,366038,243813) : difference with theory (-17) = 0
CORRECTING DEFECT 1 (vertices=146, convex hull=139, v0=198)
After retessellation of defect 1 (v0=198), euler #=-16 (122276,366315,244023) : difference with theory (-16) = 0
CORRECTING DEFECT 2 (vertices=112, convex hull=131, v0=1074)
After retessellation of defect 2 (v0=1074), euler #=-15 (122341,366575,244219) : difference with theory (-15) = 0
CORRECTING DEFECT 3 (vertices=277, convex hull=137, v0=11411)
After retessellation of defect 3 (v0=11411), euler #=-14 (122405,366829,244410) : difference with theory (-14) = 0
CORRECTING DEFECT 4 (vertices=7, convex hull=31, v0=16234)
After retessellation of defect 4 (v0=16234), euler #=-13 (122407,366845,244425) : difference with theory (-13) = 0
CORRECTING DEFECT 5 (vertices=93, convex hull=125, v0=25452)
After retessellation of defect 5 (v0=25452), euler #=-12 (122438,366998,244548) : difference with theory (-12) = 0
CORRECTING DEFECT 6 (vertices=8, convex hull=26, v0=30341)
After retessellation of defect 6 (v0=30341), euler #=-11 (122440,367012,244561) : difference with theory (-11) = 0
CORRECTING DEFECT 7 (vertices=58, convex hull=90, v0=37517)
After retessellation of defect 7 (v0=37517), euler #=-10 (122471,367145,244664) : difference with theory (-10) = 0
CORRECTING DEFECT 8 (vertices=142, convex hull=134, v0=51389)
After retessellation of defect 8 (v0=51389), euler #=-9 (122530,367392,244853) : difference with theory (-9) = 0
CORRECTING DEFECT 9 (vertices=14, convex hull=18, v0=55197)
After retessellation of defect 9 (v0=55197), euler #=-8 (122534,367409,244867) : difference with theory (-8) = 0
CORRECTING DEFECT 10 (vertices=5, convex hull=28, v0=55480)
After retessellation of defect 10 (v0=55480), euler #=-7 (122535,367419,244877) : difference with theory (-7) = 0
CORRECTING DEFECT 11 (vertices=27, convex hull=39, v0=64579)
After retessellation of defect 11 (v0=64579), euler #=-6 (122547,367470,244917) : difference with theory (-6) = 0
CORRECTING DEFECT 12 (vertices=42, convex hull=63, v0=67279)
After retessellation of defect 12 (v0=67279), euler #=-5 (122564,367548,244979) : difference with theory (-5) = 0
CORRECTING DEFECT 13 (vertices=20, convex hull=26, v0=78184)
After retessellation of defect 13 (v0=78184), euler #=-4 (122569,367571,244998) : difference with theory (-4) = 0
CORRECTING DEFECT 14 (vertices=101, convex hull=126, v0=78952)
After retessellation of defect 14 (v0=78952), euler #=-3 (122625,367792,245164) : difference with theory (-3) = 0
CORRECTING DEFECT 15 (vertices=42, convex hull=31, v0=81100)
After retessellation of defect 15 (v0=81100), euler #=-2 (122627,367812,245183) : difference with theory (-2) = 0
CORRECTING DEFECT 16 (vertices=23, convex hull=65, v0=89099)
After retessellation of defect 16 (v0=89099), euler #=-1 (122638,367868,245229) : difference with theory (-1) = 0
CORRECTING DEFECT 17 (vertices=197, convex hull=41, v0=90556)
After retessellation of defect 17 (v0=90556), euler #=0 (122650,367917,245267) : difference with theory (0) = 0
CORRECTING DEFECT 18 (vertices=6, convex hull=13, v0=90628)
After retessellation of defect 18 (v0=90628), euler #=1 (122650,367921,245272) : difference with theory (1) = 0
CORRECTING DEFECT 19 (vertices=34, convex hull=55, v0=115316)
After retessellation of defect 19 (v0=115316), euler #=2 (122665,367989,245326) : difference with theory (2) = 0
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.21 (0.08-->7.54) (max @ vno 2139 --> 2631)
face area -nan +- -nan (1000.00-->-1.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.21 (0.08-->7.54) (max @ vno 2139 --> 2631)
face area -nan +- -nan (1000.00-->-1.00)
tessellation finished, orienting corrected surface...
56 mutations (35.9%), 100 crossovers (64.1%), 15 vertices were eliminated
building final representation...
921 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=122665, nf=245326, ne=367989, g=0)
writing corrected surface to /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.orig.premesh...
0.000 % of the vertices (0 vertices) exhibit an orientation change
removing intersecting faces
000: 156 intersecting
001: 4 intersecting
terminating search with 0 intersecting
topology fixing took 1.3 minutes
FSRUNTIME@ mris_fix_topology lh 0.0211 hours 1 threads
#VMPC# mris_fix_topology VmPeak 759040
#@# Fix Topology rh Fri Jun 13 01:01:41 UTC 2025
mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 subjectname rh
reading spherical homeomorphism from 'qsphere.nofix'
reading inflated coordinates from 'inflated.nofix'
reading original coordinates from 'orig.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234
*************************************************************
Topology Correction Parameters
retessellation mode: genetic search
number of patches/generation : 10
number of generations : 10
surface mri loglikelihood coefficient : 1.0
volume mri loglikelihood coefficient : 10.0
normal dot loglikelihood coefficient : 1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution : 2
eliminate vertices during search : 1
initial patch selection : 1
select all defect vertices : 0
ordering dependant retessellation: 0
use precomputed edge table : 0
smooth retessellated patch : 2
match retessellated patch : 1
verbose mode : 0
*************************************************************
INFO: assuming .mgz format
writing corrected surface to 'orig.premesh'
7.3.2
7.3.2
before topology correction, eno=-24 (nv=123084, nf=246216, ne=369324, g=13)
using quasi-homeomorphic spherical map to tessellate cortical surface...
Correction of the Topology
Finding true center and radius of Spherical Surface...
done
Surface centered at (0,0,0) with radius 100.0 in 9 iterations
marking ambiguous vertices...
1668 ambiguous faces found in tessellation
segmenting defects...
19 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
19 defects to be corrected
0 vertices coincident
reading input surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Reading original properties of orig.nofix
Reading vertex positions of inflated.nofix
Computing Initial Surface Statistics
-face loglikelihood: -9.2790 (-4.6395)
-vertex loglikelihood: -6.3413 (-3.1706)
-normal dot loglikelihood: -3.4852 (-3.4852)
-quad curv loglikelihood: -6.0280 (-3.0140)
Total Loglikelihood : -25.1335
CORRECTING DEFECT 0 (vertices=84, convex hull=130, v0=48)
After retessellation of defect 0 (v0=48), euler #=-16 (122041,365633,243576) : difference with theory (-16) = 0
CORRECTING DEFECT 1 (vertices=127, convex hull=151, v0=243)
After retessellation of defect 1 (v0=243), euler #=-15 (122098,365879,243766) : difference with theory (-15) = 0
CORRECTING DEFECT 2 (vertices=118, convex hull=160, v0=6757)
After retessellation of defect 2 (v0=6757), euler #=-14 (122163,366141,243964) : difference with theory (-14) = 0
CORRECTING DEFECT 3 (vertices=254, convex hull=120, v0=11309)
After retessellation of defect 3 (v0=11309), euler #=-13 (122227,366392,244152) : difference with theory (-13) = 0
CORRECTING DEFECT 4 (vertices=26, convex hull=72, v0=13600)
After retessellation of defect 4 (v0=13600), euler #=-12 (122238,366450,244200) : difference with theory (-12) = 0
CORRECTING DEFECT 5 (vertices=5, convex hull=40, v0=16059)
After retessellation of defect 5 (v0=16059), euler #=-11 (122240,366466,244215) : difference with theory (-11) = 0
CORRECTING DEFECT 6 (vertices=45, convex hull=82, v0=27512)
After retessellation of defect 6 (v0=27512), euler #=-10 (122249,366530,244271) : difference with theory (-10) = 0
CORRECTING DEFECT 7 (vertices=6, convex hull=32, v0=32079)
After retessellation of defect 7 (v0=32079), euler #=-9 (122250,366544,244285) : difference with theory (-9) = 0
CORRECTING DEFECT 8 (vertices=72, convex hull=113, v0=37267)
After retessellation of defect 8 (v0=37267), euler #=-8 (122288,366703,244407) : difference with theory (-8) = 0
CORRECTING DEFECT 9 (vertices=7, convex hull=24, v0=52104)
After retessellation of defect 9 (v0=52104), euler #=-7 (122291,366719,244421) : difference with theory (-7) = 0
CORRECTING DEFECT 10 (vertices=36, convex hull=25, v0=52205)
After retessellation of defect 10 (v0=52205), euler #=-6 (122293,366733,244434) : difference with theory (-6) = 0
CORRECTING DEFECT 11 (vertices=22, convex hull=51, v0=64252)
After retessellation of defect 11 (v0=64252), euler #=-5 (122301,366776,244470) : difference with theory (-5) = 0
CORRECTING DEFECT 12 (vertices=87, convex hull=44, v0=67232)
After retessellation of defect 12 (v0=67232), euler #=-4 (122331,366881,244546) : difference with theory (-4) = 0
CORRECTING DEFECT 13 (vertices=75, convex hull=112, v0=79002)
After retessellation of defect 13 (v0=79002), euler #=-3 (122379,367068,244686) : difference with theory (-3) = 0
CORRECTING DEFECT 14 (vertices=11, convex hull=16, v0=80376)
After retessellation of defect 14 (v0=80376), euler #=-2 (122383,367084,244699) : difference with theory (-2) = 0
CORRECTING DEFECT 15 (vertices=44, convex hull=41, v0=83142)
After retessellation of defect 15 (v0=83142), euler #=-1 (122392,367126,244733) : difference with theory (-1) = 0
CORRECTING DEFECT 16 (vertices=6, convex hull=14, v0=86941)
After retessellation of defect 16 (v0=86941), euler #=0 (122393,367134,244741) : difference with theory (0) = 0
CORRECTING DEFECT 17 (vertices=23, convex hull=61, v0=88998)
After retessellation of defect 17 (v0=88998), euler #=1 (122402,367183,244782) : difference with theory (1) = 0
CORRECTING DEFECT 18 (vertices=33, convex hull=51, v0=94506)
After retessellation of defect 18 (v0=94506), euler #=2 (122417,367245,244830) : difference with theory (2) = 0
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.21 (0.12-->5.55) (max @ vno 26879 --> 31076)
face area -nan +- -nan (1000.00-->-1.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.21 (0.12-->5.55) (max @ vno 26879 --> 31076)
face area -nan +- -nan (1000.00-->-1.00)
tessellation finished, orienting corrected surface...
70 mutations (37.6%), 116 crossovers (62.4%), 35 vertices were eliminated
building final representation...
667 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=122417, nf=244830, ne=367245, g=0)
writing corrected surface to /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.orig.premesh...
0.000 % of the vertices (0 vertices) exhibit an orientation change
removing intersecting faces
000: 104 intersecting
001: 4 intersecting
002: 3 intersecting
terminating search with 0 intersecting
topology fixing took 1.2 minutes
FSRUNTIME@ mris_fix_topology rh 0.0193 hours 1 threads
#VMPC# mris_fix_topology VmPeak 758416
mris_euler_number ../surf/lh.orig.premesh
euler # = v-e+f = 2g-2: 122665 - 367989 + 245326 = 2 --> 0 holes
F =2V-4: 245326 = 245330-4 (0)
2E=3F: 735978 = 735978 (0)
total defect index = 0
mris_euler_number ../surf/rh.orig.premesh
euler # = v-e+f = 2g-2: 122417 - 367245 + 244830 = 2 --> 0 holes
F =2V-4: 244830 = 244834-4 (0)
2E=3F: 734490 = 734490 (0)
total defect index = 0
Fri Jun 13 01:02:52 UTC 2025
setenv SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
cd /tmp/tmps594ishs/freesurfer_output/subjectname/scripts
/opt/freesurfer-7.3.2/bin/defect2seg --s subjectname --cortex
freesurfer-linux-centos8_x86_64-7.3.2-20220804-6354275
defect2seg 7.3.2
Linux fv-az1121-699 6.8.0-1029-azure #34~22.04.1-Ubuntu SMP Thu May 1 02:51:54 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux
pid 10710
mri_label2label --label-cortex /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.orig.nofix /tmp/tmps594ishs/freesurfer_output/subjectname/mri/aseg.presurf.mgz 0 /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.nofix.cortex.label
Generating cortex label... RemoveHipAmgy=0
NucAccIsMedialWall=0
mris->useRealRAS=0
13 non-cortical segments detected
only using segment with 7277 vertices
erasing segment 1 (vno[0] = 51162)
erasing segment 2 (vno[0] = 87031)
erasing segment 3 (vno[0] = 87917)
erasing segment 4 (vno[0] = 88800)
erasing segment 5 (vno[0] = 88816)
erasing segment 6 (vno[0] = 89716)
erasing segment 7 (vno[0] = 90465)
erasing segment 8 (vno[0] = 90506)
erasing segment 9 (vno[0] = 90553)
erasing segment 10 (vno[0] = 91254)
erasing segment 11 (vno[0] = 91336)
erasing segment 12 (vno[0] = 96325)
mri_label2vol --defects /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.orig.nofix /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.defect_labels /tmp/tmps594ishs/freesurfer_output/subjectname/mri/orig.mgz 1000 0 /tmp/tmps594ishs/freesurfer_output/subjectname/mri/surface.defects.mgz /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.nofix.cortex.label
mri_label2vol supposed to be reproducible but seed not set
Contraining to label /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.nofix.cortex.label
Changing input type 0 to MRI_INT
Converting defects to volume: offset=1000, merge=0
Writing to /tmp/tmps594ishs/freesurfer_output/subjectname/mri/surface.defects.mgz
mris_defects_pointset -s /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.orig.nofix -d /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.defect_labels -o /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.defects.pointset --label /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.nofix.cortex.label
Reading in surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.orig.nofix
Reading in defect segmentation /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.defect_labels
Reading in label /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.nofix.cortex.label
#VMPC# mris_defects_pointset 183988
mris_defects_pointset done
mri_label2label --label-cortex /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.orig.nofix /tmp/tmps594ishs/freesurfer_output/subjectname/mri/aseg.presurf.mgz 0 /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.nofix.cortex.label
Generating cortex label... RemoveHipAmgy=0
NucAccIsMedialWall=0
mris->useRealRAS=0
10 non-cortical segments detected
only using segment with 7387 vertices
erasing segment 1 (vno[0] = 77456)
erasing segment 2 (vno[0] = 80482)
erasing segment 3 (vno[0] = 81383)
erasing segment 4 (vno[0] = 83222)
erasing segment 5 (vno[0] = 90415)
erasing segment 6 (vno[0] = 92093)
erasing segment 7 (vno[0] = 92983)
erasing segment 8 (vno[0] = 103940)
erasing segment 9 (vno[0] = 107995)
mri_label2vol --defects /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.orig.nofix /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.defect_labels /tmp/tmps594ishs/freesurfer_output/subjectname/mri/surface.defects.mgz 2000 1 /tmp/tmps594ishs/freesurfer_output/subjectname/mri/surface.defects.mgz /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.nofix.cortex.label
mri_label2vol supposed to be reproducible but seed not set
Contraining to label /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.nofix.cortex.label
Converting defects to volume: offset=2000, merge=1
Writing to /tmp/tmps594ishs/freesurfer_output/subjectname/mri/surface.defects.mgz
mris_defects_pointset -s /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.orig.nofix -d /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.defect_labels -o /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.defects.pointset --label /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.nofix.cortex.label
Reading in surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.orig.nofix
Reading in defect segmentation /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.defect_labels
Reading in label /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.nofix.cortex.label
#VMPC# mris_defects_pointset 183408
mris_defects_pointset done
Started at Fri Jun 13 01:02:52 UTC 2025
Ended at Fri Jun 13 01:03:15 UTC 2025
Defect2seg-Run-Time-Sec 23
Defect2seg-Run-Time-Min 0.46
Defect2seg-Run-Time-Hours 0.01
tkmeditfv subjectname brain.finalsurfs.mgz -defect
defect2seg Done
mris_remesh --remesh --iters 3 --input /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.orig.premesh --output /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.orig
iters = 3
standard remeshing without target
adjusted l: 0.714492
remeshing to edge length 0.714492 with 3 iterations
avg qual before : 0.893529 after: 0.971044
Removing intersections
Remeshed surface quality stats nv0 = 122665 nv = 128612 1.04848
Area 257220 0.30578 0.03410 0.073937 0.4764
Corner 771660 60.00000 8.82459 15.341482 145.9457
Edge 385830 0.84839 0.08303 0.458717 1.2680
Hinge 385830 8.78222 9.21839 0.000007 172.2284
mris_remesh done
mris_remesh --remesh --iters 3 --input /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.orig.premesh --output /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.orig
iters = 3
standard remeshing without target
adjusted l: 0.714266
remeshing to edge length 0.714266 with 3 iterations
avg qual before : 0.89368 after: 0.971137
Removing intersections
Remeshed surface quality stats nv0 = 122417 nv = 128513 1.0498
Area 257022 0.30539 0.03388 0.081315 0.4832
Corner 771066 60.00000 8.80726 16.307931 146.9377
Edge 385533 0.84783 0.08275 0.499427 1.2603
Hinge 385533 8.77716 9.20482 0.000002 126.6836
mris_remesh done
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
intersection removal took 0.00 hours
writing corrected surface to ../surf/lh.orig
rm -f ../surf/lh.inflated
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
intersection removal took 0.00 hours
writing corrected surface to ../surf/rh.orig
rm -f ../surf/rh.inflated
#--------------------------------------------
#@# AutoDetGWStats lh Fri Jun 13 01:04:02 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh
7.3.2
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
setenv SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh
border white: 237138 voxels (1.41%)
border gray 253932 voxels (1.51%)
Reading in intensity volume brain.finalsurfs.mgz
Reading in wm volume wm.mgz
Reading in surf ../surf/lh.orig.premesh
Auto detecting stats
MRIclipBrightWM(): nthresh=15301, wmmin=5, clip=110
Binarizing thresholding at 5
computing class statistics... low=30, hi=110.000000
CCS WM (100.0): 99.9 +- 7.7 [70.0 --> 110.0]
CCS GM (76.0) : 74.9 +- 10.5 [30.0 --> 110.0]
white_mean = 99.9153 +/- 7.71489, gray_mean = 74.9016 +/- 10.5005
using class modes intead of means, discounting robust sigmas....
MRIScomputeClassModes(): min=0 max=179 nbins=180
intensity peaks found at WM=104+-4.3, GM=71+-9.6
white_mode = 104, gray_mode = 71
std_scale = 1
Applying sanity checks, max_scale_down = 0.2
setting MIN_GRAY_AT_WHITE_BORDER to 60.5 (was 70.000000)
setting MAX_BORDER_WHITE to 111.7 (was 105.000000)
setting MIN_BORDER_WHITE to 71.0 (was 85.000000)
setting MAX_CSF to 50.0 (was 40.000000)
setting MAX_GRAY to 96.3 (was 95.000000)
setting MAX_GRAY_AT_CSF_BORDER to 60.5 (was 75.000000)
setting MIN_GRAY_AT_CSF_BORDER to 39.5 (was 40.000000)
When placing the white surface
white_border_hi = 111.715;
white_border_low = 71;
white_outside_low = 60.4995;
white_inside_hi = 120;
white_outside_hi = 111.715;
When placing the pial surface
pial_border_hi = 60.4995;
pial_border_low = 39.4984;
pial_outside_low = 10;
pial_inside_hi = 96.2851;
pial_outside_hi = 55.2492;
#VMPC# mris_autodet_gwstats VmPeak 255984
mris_autodet_gwstats done
#--------------------------------------------
#@# AutoDetGWStats rh Fri Jun 13 01:04:05 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh
7.3.2
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
setenv SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh
border white: 237138 voxels (1.41%)
border gray 253932 voxels (1.51%)
Reading in intensity volume brain.finalsurfs.mgz
Reading in wm volume wm.mgz
Reading in surf ../surf/rh.orig.premesh
Auto detecting stats
MRIclipBrightWM(): nthresh=15301, wmmin=5, clip=110
Binarizing thresholding at 5
computing class statistics... low=30, hi=110.000000
CCS WM (100.0): 99.9 +- 7.7 [70.0 --> 110.0]
CCS GM (76.0) : 74.9 +- 10.5 [30.0 --> 110.0]
white_mean = 99.9153 +/- 7.71489, gray_mean = 74.9016 +/- 10.5005
using class modes intead of means, discounting robust sigmas....
MRIScomputeClassModes(): min=0 max=179 nbins=180
intensity peaks found at WM=104+-4.3, GM=72+-9.6
white_mode = 104, gray_mode = 72
std_scale = 1
Applying sanity checks, max_scale_down = 0.2
setting MIN_GRAY_AT_WHITE_BORDER to 61.5 (was 70.000000)
setting MAX_BORDER_WHITE to 111.7 (was 105.000000)
setting MIN_BORDER_WHITE to 72.0 (was 85.000000)
setting MAX_CSF to 51.0 (was 40.000000)
setting MAX_GRAY to 96.3 (was 95.000000)
setting MAX_GRAY_AT_CSF_BORDER to 61.5 (was 75.000000)
setting MIN_GRAY_AT_CSF_BORDER to 40.5 (was 40.000000)
When placing the white surface
white_border_hi = 111.715;
white_border_low = 72;
white_outside_low = 61.4995;
white_inside_hi = 120;
white_outside_hi = 111.715;
When placing the pial surface
pial_border_hi = 61.4995;
pial_border_low = 40.4984;
pial_outside_low = 10;
pial_inside_hi = 96.2851;
pial_outside_hi = 56.2492;
#VMPC# mris_autodet_gwstats VmPeak 255636
mris_autodet_gwstats done
#--------------------------------------------
#@# WhitePreAparc lh Fri Jun 13 01:04:09 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5
7.3.2
7.3.2
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
setenv SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5
Reading in input surface ../surf/lh.orig
Smoothing surface before ripping with 5 iterations
Area 257220 0.27489 0.06201 0.001717 0.6114
Corner 771660 60.00000 9.08771 8.197482 148.5087
Edge 385830 0.80040 0.11111 0.048691 1.2764
Hinge 385830 5.94967 5.97972 0.000017 143.2159
Not reading in aparc
Reading in input volume brain.finalsurfs.mgz
Reading in wm volume wm.mgz
MRIclipBrightWM(): nthresh=15301, wmmin=5, clip=110
MRIfindBrightNonWM(): 1607 bright non-wm voxels segmented.
Masking bright non-wm for white surface
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
Reading in seg volume aseg.presurf.mgz
Ripping frozen voxels
INFO: rip surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures...
which=1, fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=0
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=6302, nmarked2=4, nripped=6302
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247
MRISripSegs(): -2 2 0.5 ripped 0
vertex 64306: xyz = (-30.9915,-10.7611,6.09681) oxyz = (-30.9915,-10.7611,6.09681) wxzy = (-30.9915,-10.7611,6.09681) pxyz = (0,0,0)
CBVO Creating mask 128612
n_averages 4
Iteration 0 =========================================
n_averages=4, current_sigma=2
Freezing midline and others
Ripping frozen voxels
INFO: rip surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures...
which=1, fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=6302
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=6302, nmarked2=4, nripped=6302
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247
MRISripSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000;
border_hi = 111.7148900;
border_low = 71.0000000;
outside_low = 60.4994740;
outside_hi = 111.7148900;
sigma = 2;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128612
Gdiag_no=-1
vno start=0, stop=128612
Replacing 255s with 0s
#SI# sigma=2 had to be increased for 90 vertices, nripped=6302
mean border=81.8, 59 (59) missing vertices, mean dist 0.4 [0.6 (%33.7)->0.9 (%66.3))]
%61 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.2027 min
Finding expansion regions
mean absolute distance = 0.81 +- 0.98
2912 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=2.0, host=fv-az, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 100
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0
000: dt: 0.0000, sse=3281563.8, rms=11.329
001: dt: 0.5000, sse=1822606.0, rms=8.292 (26.805%)
002: dt: 0.5000, sse=1079192.5, rms=6.195 (25.295%)
003: dt: 0.5000, sse=686300.5, rms=4.720 (23.798%)
004: dt: 0.5000, sse=493150.2, rms=3.787 (19.770%)
005: dt: 0.5000, sse=405780.2, rms=3.270 (13.667%)
006: dt: 0.5000, sse=370697.5, rms=3.031 (7.291%)
007: dt: 0.5000, sse=358622.7, rms=2.925 (3.509%)
rms = 2.8792/2.9248, sse=354507.9/358622.7, time step reduction 1 of 3 to 0.250 0 0 1
008: dt: 0.5000, sse=354507.9, rms=2.879 (1.561%)
009: dt: 0.2500, sse=213733.7, rms=1.610 (44.096%)
010: dt: 0.2500, sse=197879.5, rms=1.351 (16.042%)
011: dt: 0.2500, sse=189937.9, rms=1.272 (5.896%)
rms = 1.2301/1.2717, sse=193458.7/189937.9, time step reduction 2 of 3 to 0.125 0 1 1
012: dt: 0.2500, sse=193458.7, rms=1.230 (3.269%)
013: dt: 0.1250, sse=186392.3, rms=1.171 (4.779%)
rms = 1.1603/1.1713, sse=183875.5/186392.3, time step reduction 3 of 3 to 0.062 0 0 1
014: dt: 0.1250, sse=183875.5, rms=1.160 (0.943%)
maximum number of reductions reached, breaking from loop
positioning took 1.0 minutes
Iteration 1 =========================================
n_averages=2, current_sigma=1
Freezing midline and others
Ripping frozen voxels
INFO: rip surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures...
which=1, fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=6302
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=6540, nmarked2=5, nripped=6540
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247
MRISripSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000;
border_hi = 111.7148900;
border_low = 71.0000000;
outside_low = 60.4994740;
outside_hi = 111.7148900;
sigma = 1;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128612
Gdiag_no=-1
vno start=0, stop=128612
Replacing 255s with 0s
#SI# sigma=1 had to be increased for 42 vertices, nripped=6540
mean border=85.6, 63 (1) missing vertices, mean dist -0.3 [0.5 (%76.0)->0.2 (%24.0))]
%74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.1421 min
Finding expansion regions
mean absolute distance = 0.45 +- 0.71
4458 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=1.0, host=fv-az, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=1032054.0, rms=5.861
015: dt: 0.5000, sse=627839.6, rms=4.200 (28.338%)
016: dt: 0.5000, sse=506827.0, rms=3.595 (14.409%)
017: dt: 0.5000, sse=445639.7, rms=3.210 (10.721%)
018: dt: 0.5000, sse=414914.5, rms=2.998 (6.590%)
019: dt: 0.5000, sse=384855.1, rms=2.794 (6.815%)
rms = 2.7768/2.7939, sse=379507.5/384855.1, time step reduction 1 of 3 to 0.250 0 0 1
020: dt: 0.5000, sse=379507.5, rms=2.777 (0.613%)
021: dt: 0.2500, sse=234942.8, rms=1.308 (52.890%)
022: dt: 0.2500, sse=220077.4, rms=1.037 (20.752%)
023: dt: 0.2500, sse=216465.2, rms=0.958 (7.563%)
rms = 0.9216/0.9583, sse=214156.9/216465.2, time step reduction 2 of 3 to 0.125 0 0 1
024: dt: 0.2500, sse=214156.9, rms=0.922 (3.824%)
rms = 0.8710/0.9216, sse=215440.1/214156.9, time step reduction 3 of 3 to 0.062 0 1 0
025: dt: 0.1250, sse=215440.1, rms=0.871 (5.494%)
maximum number of reductions reached, breaking from loop
positioning took 0.7 minutes
Iteration 2 =========================================
n_averages=1, current_sigma=0.5
Freezing midline and others
Ripping frozen voxels
INFO: rip surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures...
which=1, fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=6540
removing 4 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=6590, nmarked2=6, nripped=6590
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247
MRISripSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000;
border_hi = 111.7148900;
border_low = 71.0000000;
outside_low = 60.4994740;
outside_hi = 111.7148900;
sigma = 0.5;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128612
Gdiag_no=-1
vno start=0, stop=128612
Replacing 255s with 0s
#SI# sigma=0.5 had to be increased for 45 vertices, nripped=6590
mean border=87.9, 76 (0) missing vertices, mean dist -0.2 [0.3 (%73.6)->0.2 (%26.4))]
%83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0799 min
Finding expansion regions
mean absolute distance = 0.27 +- 0.42
3083 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.5, host=fv-az, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=465093.0, rms=3.356
026: dt: 0.5000, sse=334338.8, rms=2.414 (28.061%)
rms = 2.3865/2.4142, sse=330201.6/334338.8, time step reduction 1 of 3 to 0.250 0 0 1
027: dt: 0.5000, sse=330201.6, rms=2.387 (1.146%)
028: dt: 0.2500, sse=227477.6, rms=1.156 (51.541%)
029: dt: 0.2500, sse=217004.0, rms=0.963 (16.768%)
030: dt: 0.2500, sse=213663.0, rms=0.899 (6.571%)
rms = 0.8826/0.8993, sse=213604.9/213663.0, time step reduction 2 of 3 to 0.125 0 0 1
031: dt: 0.2500, sse=213604.9, rms=0.883 (1.862%)
032: dt: 0.1250, sse=207980.4, rms=0.797 (9.743%)
rms = 0.7903/0.7966, sse=208476.0/207980.4, time step reduction 3 of 3 to 0.062 0 1 1
033: dt: 0.1250, sse=208476.0, rms=0.790 (0.784%)
maximum number of reductions reached, breaking from loop
positioning took 0.5 minutes
Iteration 3 =========================================
n_averages=0, current_sigma=0.25
Freezing midline and others
Ripping frozen voxels
INFO: rip surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures...
which=1, fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=6590
removing 2 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=6642, nmarked2=7, nripped=6642
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247
MRISripSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000;
border_hi = 111.7148900;
border_low = 71.0000000;
outside_low = 60.4994740;
outside_hi = 111.7148900;
sigma = 0.25;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128612
Gdiag_no=-1
vno start=0, stop=128612
Replacing 255s with 0s
#SI# sigma=0.25 had to be increased for 34 vertices, nripped=6642
mean border=88.6, 86 (0) missing vertices, mean dist -0.0 [0.2 (%57.9)->0.2 (%42.1))]
%86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0502 min
Finding expansion regions
mean absolute distance = 0.20 +- 0.31
2923 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.2, host=fv-az, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=235735.9, rms=1.369
034: dt: 0.5000, sse=226493.6, rms=1.230 (10.204%)
rms = 1.6233/1.2297, sse=251911.8/226493.6, time step reduction 1 of 3 to 0.250 0 1 1
RMS increased, rejecting step
035: dt: 0.2500, sse=203534.5, rms=0.784 (36.208%)
036: dt: 0.2500, sse=202779.4, rms=0.645 (17.778%)
rms = 0.6212/0.6450, sse=203488.2/202779.4, time step reduction 2 of 3 to 0.125 0 1 1
037: dt: 0.2500, sse=203488.2, rms=0.621 (3.691%)
rms = 0.5862/0.6212, sse=197685.3/203488.2, time step reduction 3 of 3 to 0.062 0 0 1
038: dt: 0.1250, sse=197685.3, rms=0.586 (5.636%)
maximum number of reductions reached, breaking from loop
positioning took 0.4 minutes
Writing output to ../surf/lh.white.preaparc
#ET# mris_place_surface 3.06 minutes
#VMPC# mris_place_surfaces VmPeak 2118176
mris_place_surface done
#--------------------------------------------
#@# WhitePreAparc rh Fri Jun 13 01:07:18 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5
7.3.2
7.3.2
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
setenv SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5
Reading in input surface ../surf/rh.orig
Smoothing surface before ripping with 5 iterations
Area 257022 0.27447 0.06184 0.011393 0.5992
Corner 771066 60.00000 9.04729 16.744599 137.0922
Edge 385533 0.79977 0.11083 0.138855 1.3532
Hinge 385533 5.95507 5.97774 0.000023 135.9850
Not reading in aparc
Reading in input volume brain.finalsurfs.mgz
Reading in wm volume wm.mgz
MRIclipBrightWM(): nthresh=15301, wmmin=5, clip=110
MRIfindBrightNonWM(): 1607 bright non-wm voxels segmented.
Masking bright non-wm for white surface
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
Reading in seg volume aseg.presurf.mgz
Ripping frozen voxels
INFO: rip surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures...
which=1, fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=0
removing 3 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=6408, nmarked2=0, nripped=6408
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247
MRISripSegs(): -2 2 0.5 ripped 0
vertex 64257: xyz = (54.8197,-10.0048,35.8937) oxyz = (54.8197,-10.0048,35.8937) wxzy = (54.8197,-10.0048,35.8937) pxyz = (0,0,0)
CBVO Creating mask 128513
n_averages 4
Iteration 0 =========================================
n_averages=4, current_sigma=2
Freezing midline and others
Ripping frozen voxels
INFO: rip surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures...
which=1, fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=6408
removing 3 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=6408, nmarked2=0, nripped=6408
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247
MRISripSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000;
border_hi = 111.7148900;
border_low = 72.0000000;
outside_low = 61.4994740;
outside_hi = 111.7148900;
sigma = 2;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128513
Gdiag_no=-1
vno start=0, stop=128513
Replacing 255s with 0s
#SI# sigma=2 had to be increased for 25 vertices, nripped=6408
mean border=82.3, 27 (27) missing vertices, mean dist 0.3 [0.7 (%35.1)->0.9 (%64.9))]
%58 local maxima, %37 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.1999 min
Finding expansion regions
mean absolute distance = 0.80 +- 0.99
2807 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=2.0, host=fv-az, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 100
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0
000: dt: 0.0000, sse=3261747.0, rms=11.302
001: dt: 0.5000, sse=1781949.9, rms=8.197 (27.476%)
002: dt: 0.5000, sse=1042354.2, rms=6.076 (25.871%)
003: dt: 0.5000, sse=663757.8, rms=4.624 (23.896%)
004: dt: 0.5000, sse=477331.2, rms=3.704 (19.903%)
005: dt: 0.5000, sse=393044.5, rms=3.190 (13.861%)
006: dt: 0.5000, sse=357484.3, rms=2.951 (7.504%)
007: dt: 0.5000, sse=346692.7, rms=2.848 (3.494%)
rms = 2.8075/2.8479, sse=339116.0/346692.7, time step reduction 1 of 3 to 0.250 0 0 1
008: dt: 0.5000, sse=339116.0, rms=2.808 (1.419%)
009: dt: 0.2500, sse=201583.4, rms=1.461 (47.950%)
010: dt: 0.2500, sse=184584.9, rms=1.174 (19.694%)
011: dt: 0.2500, sse=179040.2, rms=1.091 (7.043%)
rms = 1.0461/1.0909, sse=176452.0/179040.2, time step reduction 2 of 3 to 0.125 0 0 1
012: dt: 0.2500, sse=176452.0, rms=1.046 (4.102%)
013: dt: 0.1250, sse=174330.8, rms=0.984 (5.912%)
rms = 0.9728/0.9843, sse=175666.7/174330.8, time step reduction 3 of 3 to 0.062 0 1 1
014: dt: 0.1250, sse=175666.7, rms=0.973 (1.163%)
maximum number of reductions reached, breaking from loop
positioning took 1.0 minutes
Iteration 1 =========================================
n_averages=2, current_sigma=1
Freezing midline and others
Ripping frozen voxels
INFO: rip surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures...
which=1, fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=6408
removing 2 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=6652, nmarked2=0, nripped=6652
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247
MRISripSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000;
border_hi = 111.7148900;
border_low = 72.0000000;
outside_low = 61.4994740;
outside_hi = 111.7148900;
sigma = 1;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128513
Gdiag_no=-1
vno start=0, stop=128513
Replacing 255s with 0s
#SI# sigma=1 had to be increased for 38 vertices, nripped=6652
mean border=86.0, 71 (6) missing vertices, mean dist -0.3 [0.5 (%75.2)->0.2 (%24.8))]
%72 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.1396 min
Finding expansion regions
mean absolute distance = 0.44 +- 0.72
4302 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=1.0, host=fv-az, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=982699.4, rms=5.688
015: dt: 0.5000, sse=599104.4, rms=4.094 (28.034%)
016: dt: 0.5000, sse=489103.0, rms=3.507 (14.328%)
017: dt: 0.5000, sse=433305.1, rms=3.160 (9.888%)
018: dt: 0.5000, sse=404448.4, rms=2.970 (6.006%)
019: dt: 0.5000, sse=379583.4, rms=2.784 (6.274%)
rms = 2.7653/2.7841, sse=376065.3/379583.4, time step reduction 1 of 3 to 0.250 0 0 1
020: dt: 0.5000, sse=376065.3, rms=2.765 (0.677%)
021: dt: 0.2500, sse=232462.6, rms=1.293 (53.238%)
022: dt: 0.2500, sse=216780.0, rms=1.015 (21.483%)
023: dt: 0.2500, sse=214919.4, rms=0.932 (8.188%)
rms = 0.8931/0.9322, sse=215157.1/214919.4, time step reduction 2 of 3 to 0.125 0 1 1
024: dt: 0.2500, sse=215157.1, rms=0.893 (4.189%)
rms = 0.8434/0.8931, sse=209640.9/215157.1, time step reduction 3 of 3 to 0.062 0 0 1
025: dt: 0.1250, sse=209640.9, rms=0.843 (5.563%)
maximum number of reductions reached, breaking from loop
positioning took 0.7 minutes
Iteration 2 =========================================
n_averages=1, current_sigma=0.5
Freezing midline and others
Ripping frozen voxels
INFO: rip surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures...
which=1, fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=6652
removing 3 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=6676, nmarked2=0, nripped=6676
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247
MRISripSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000;
border_hi = 111.7148900;
border_low = 72.0000000;
outside_low = 61.4994740;
outside_hi = 111.7148900;
sigma = 0.5;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128513
Gdiag_no=-1
vno start=0, stop=128513
Replacing 255s with 0s
#SI# sigma=0.5 had to be increased for 37 vertices, nripped=6676
mean border=88.2, 56 (3) missing vertices, mean dist -0.2 [0.3 (%73.2)->0.2 (%26.8))]
%81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0782 min
Finding expansion regions
mean absolute distance = 0.26 +- 0.43
2817 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.5, host=fv-az, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=441784.5, rms=3.240
026: dt: 0.5000, sse=318648.1, rms=2.327 (28.169%)
rms = 2.3291/2.3273, sse=318591.0/318648.1, time step reduction 1 of 3 to 0.250 0 0 1
RMS increased, rejecting step
027: dt: 0.2500, sse=250204.0, rms=1.618 (30.476%)
028: dt: 0.2500, sse=213275.4, rms=1.056 (34.730%)
029: dt: 0.2500, sse=204663.1, rms=0.871 (17.493%)
rms = 0.8228/0.8714, sse=202642.3/204663.1, time step reduction 2 of 3 to 0.125 0 0 1
030: dt: 0.2500, sse=202642.3, rms=0.823 (5.578%)
rms = 0.7806/0.8228, sse=200851.9/202642.3, time step reduction 3 of 3 to 0.062 0 0 1
031: dt: 0.1250, sse=200851.9, rms=0.781 (5.128%)
maximum number of reductions reached, breaking from loop
positioning took 0.4 minutes
Iteration 3 =========================================
n_averages=0, current_sigma=0.25
Freezing midline and others
Ripping frozen voxels
INFO: rip surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures...
which=1, fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=6676
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=6685, nmarked2=0, nripped=6685
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247
MRISripSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000;
border_hi = 111.7148900;
border_low = 72.0000000;
outside_low = 61.4994740;
outside_hi = 111.7148900;
sigma = 0.25;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128513
Gdiag_no=-1
vno start=0, stop=128513
Replacing 255s with 0s
#SI# sigma=0.25 had to be increased for 48 vertices, nripped=6685
mean border=88.9, 61 (2) missing vertices, mean dist -0.0 [0.2 (%57.8)->0.2 (%42.2))]
%84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0496 min
Finding expansion regions
mean absolute distance = 0.20 +- 0.31
2721 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.2, host=fv-az, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=227221.2, rms=1.343
032: dt: 0.5000, sse=221451.0, rms=1.229 (8.512%)
rms = 1.6243/1.2287, sse=247634.7/221451.0, time step reduction 1 of 3 to 0.250 0 1 1
RMS increased, rejecting step
033: dt: 0.2500, sse=199713.8, rms=0.798 (35.059%)
034: dt: 0.2500, sse=195598.2, rms=0.682 (14.562%)
rms = 0.6494/0.6817, sse=193634.6/195598.2, time step reduction 2 of 3 to 0.125 0 0 1
035: dt: 0.2500, sse=193634.6, rms=0.649 (4.741%)
rms = 0.6184/0.6494, sse=194650.0/193634.6, time step reduction 3 of 3 to 0.062 0 1 1
036: dt: 0.1250, sse=194650.0, rms=0.618 (4.771%)
maximum number of reductions reached, breaking from loop
positioning took 0.4 minutes
Writing output to ../surf/rh.white.preaparc
#ET# mris_place_surface 2.96 minutes
#VMPC# mris_place_surfaces VmPeak 2095484
mris_place_surface done
#--------------------------------------------
#@# CortexLabel lh Fri Jun 13 01:10:20 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 0 ../label/lh.cortex.label
Generating cortex label... RemoveHipAmgy=0
NucAccIsMedialWall=0
mris->useRealRAS=0
6 non-cortical segments detected
only using segment with 7999 vertices
erasing segment 0 (vno[0] = 27085)
erasing segment 1 (vno[0] = 28830)
erasing segment 3 (vno[0] = 46022)
erasing segment 4 (vno[0] = 77142)
erasing segment 5 (vno[0] = 79900)
#--------------------------------------------
#@# CortexLabel+HipAmyg lh Fri Jun 13 01:10:30 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 1 ../label/lh.cortex+hipamyg.label
Generating cortex label... RemoveHipAmgy=1
NucAccIsMedialWall=0
mris->useRealRAS=0
9 non-cortical segments detected
only using segment with 6353 vertices
erasing segment 0 (vno[0] = 27085)
erasing segment 1 (vno[0] = 28830)
erasing segment 3 (vno[0] = 46022)
erasing segment 4 (vno[0] = 72454)
erasing segment 5 (vno[0] = 72475)
erasing segment 6 (vno[0] = 77142)
erasing segment 7 (vno[0] = 77149)
erasing segment 8 (vno[0] = 79900)
#--------------------------------------------
#@# CortexLabel rh Fri Jun 13 01:10:40 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 0 ../label/rh.cortex.label
Generating cortex label... RemoveHipAmgy=0
NucAccIsMedialWall=0
mris->useRealRAS=0
2 non-cortical segments detected
only using segment with 8066 vertices
erasing segment 1 (vno[0] = 77348)
#--------------------------------------------
#@# CortexLabel+HipAmyg rh Fri Jun 13 01:10:50 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 1 ../label/rh.cortex+hipamyg.label
Generating cortex label... RemoveHipAmgy=1
NucAccIsMedialWall=0
mris->useRealRAS=0
3 non-cortical segments detected
only using segment with 6327 vertices
erasing segment 1 (vno[0] = 77348)
erasing segment 2 (vno[0] = 117671)
#--------------------------------------------
#@# Smooth2 lh Fri Jun 13 01:11:00 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm
smoothing for 3 iterations
setting seed for random number generator to 1234
smoothing surface tessellation for 3 iterations...
smoothing complete - recomputing first and second fundamental forms...
#--------------------------------------------
#@# Smooth2 rh Fri Jun 13 01:11:03 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm
smoothing for 3 iterations
setting seed for random number generator to 1234
smoothing surface tessellation for 3 iterations...
smoothing complete - recomputing first and second fundamental forms...
#--------------------------------------------
#@# Inflation2 lh Fri Jun 13 01:11:05 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated
Reading ../surf/lh.smoothwm
avg radius = 46.9 mm, total surface area = 79403 mm^2
step 005: RMS=0.109 (target=0.015)
step 010: RMS=0.080 (target=0.015)
step 015: RMS=0.067 (target=0.015)
step 020: RMS=0.057 (target=0.015)
step 025: RMS=0.047 (target=0.015)
step 030: RMS=0.039 (target=0.015)
step 035: RMS=0.033 (target=0.015)
step 040: RMS=0.028 (target=0.015)
step 045: RMS=0.025 (target=0.015)
step 050: RMS=0.022 (target=0.015)
step 055: RMS=0.020 (target=0.015)
step 060: RMS=0.019 (target=0.015) writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc
inflation complete.
inflation took 0.3 minutes
mris_inflate utimesec 14.864329
mris_inflate stimesec 0.089007
mris_inflate ru_maxrss 199920
mris_inflate ru_ixrss 0
mris_inflate ru_idrss 0
mris_inflate ru_isrss 0
mris_inflate ru_minflt 31737
mris_inflate ru_majflt 53
mris_inflate ru_nswap 0
mris_inflate ru_inblock 0
mris_inflate ru_oublock 10056
mris_inflate ru_msgsnd 0
mris_inflate ru_msgrcv 0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw 320
mris_inflate ru_nivcsw 67
#--------------------------------------------
#@# Inflation2 rh Fri Jun 13 01:11:20 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated
Reading ../surf/rh.smoothwm
avg radius = 46.8 mm, total surface area = 79169 mm^2
step 005: RMS=0.108 (target=0.015)
step 010: RMS=0.080 (target=0.015)
step 015: RMS=0.068 (target=0.015)
step 020: RMS=0.057 (target=0.015)
step 025: RMS=0.047 (target=0.015)
step 030: RMS=0.039 (target=0.015)
step 035: RMS=0.033 (target=0.015)
step 040: RMS=0.029 (target=0.015)
step 045: RMS=0.026 (target=0.015)
step 050: RMS=0.023 (target=0.015)
step 055: RMS=0.021 (target=0.015)
step 060: RMS=0.019 (target=0.015) writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc
inflation complete.
inflation took 0.2 minutes
mris_inflate utimesec 14.709197
mris_inflate stimesec 0.070010
mris_inflate ru_maxrss 199660
mris_inflate ru_ixrss 0
mris_inflate ru_idrss 0
mris_inflate ru_isrss 0
mris_inflate ru_minflt 30648
mris_inflate ru_majflt 13
mris_inflate ru_nswap 0
mris_inflate ru_inblock 0
mris_inflate ru_oublock 10048
mris_inflate ru_msgsnd 0
mris_inflate ru_msgrcv 0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw 297
mris_inflate ru_nivcsw 57
#--------------------------------------------
#@# Curv .H and .K lh Fri Jun 13 01:11:35 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/surf
mris_curvature -w -seed 1234 lh.white.preaparc
setting seed for random number generator to 1234
total integrated curvature = 23.376*4pi (293.755) --> -22 handles
ICI = 116.3, FI = 1118.8, variation=17585.305
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
rm -f lh.white.K
ln -s lh.white.preaparc.K lh.white.K
mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated
setting seed for random number generator to 1234
normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
209 vertices thresholded to be in k1 ~ [-0.21 0.33], k2 ~ [-0.10 0.07]
total integrated curvature = 0.511*4pi (6.418) --> 0 handles
ICI = 1.5, FI = 9.1, variation=160.850
125 vertices thresholded to be in [-0.01 0.02]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
154 vertices thresholded to be in [-0.13 0.17]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.024
done.
#--------------------------------------------
#@# Curv .H and .K rh Fri Jun 13 01:12:15 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/surf
mris_curvature -w -seed 1234 rh.white.preaparc
setting seed for random number generator to 1234
total integrated curvature = 21.866*4pi (274.781) --> -21 handles
ICI = 114.1, FI = 1111.6, variation=17451.587
writing Gaussian curvature to ./rh.white.preaparc.K...done.
writing mean curvature to ./rh.white.preaparc.H...done.
rm -f rh.white.H
ln -s rh.white.preaparc.H rh.white.H
rm -f rh.white.K
ln -s rh.white.preaparc.K rh.white.K
mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated
setting seed for random number generator to 1234
normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
170 vertices thresholded to be in k1 ~ [-0.26 0.35], k2 ~ [-0.11 0.08]
total integrated curvature = 0.480*4pi (6.029) --> 1 handles
ICI = 1.5, FI = 9.2, variation=162.592
109 vertices thresholded to be in [-0.01 0.02]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
139 vertices thresholded to be in [-0.14 0.17]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.024
done.
#--------------------------------------------
#@# Sphere lh Fri Jun 13 01:12:55 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
setting seed for random number genererator to 1234
version: 7.3.2
available threads: 1
reading original vertex positions...
projecting onto sphere...
surface projected - minimizing metric distortion...
scaling brain by 0.296...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=fv-az, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
--------------------
mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %20.91
pass 1: epoch 2 of 3 starting distance error %20.87
unfolding complete - removing small folds...
starting distance error %20.81
removing remaining folds...
final distance error %20.85
MRISunfold() return, current seed 1234
-01: dt=0.0000, 4 negative triangles VmPeak 537600
174: dt=0.9900, 4 negative triangles
175: dt=0.9900, 2 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 0.1180 hours
FSRUNTIME@ mris_sphere 0.1180 hours 1 threads
#VMPC# mris_sphere VmPeak 537600
mris_sphere done
#--------------------------------------------
#@# Sphere rh Fri Jun 13 01:20:00 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere
setting seed for random number genererator to 1234
version: 7.3.2
available threads: 1
reading original vertex positions...
projecting onto sphere...
surface projected - minimizing metric distortion...
scaling brain by 0.296...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=fv-az, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 1234
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
--------------------
mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %20.91
pass 1: epoch 2 of 3 starting distance error %20.90
unfolding complete - removing small folds...
starting distance error %20.85
removing remaining folds...
final distance error %20.85
MRISunfold() return, current seed 1234
-01: dt=0.0000, 141 negative triangles VmPeak 537372
091: dt=0.9900, 141 negative triangles
092: dt=0.9900, 72 negative triangles
093: dt=0.9900, 53 negative triangles
094: dt=0.9900, 36 negative triangles
095: dt=0.9900, 41 negative triangles
096: dt=0.9900, 27 negative triangles
097: dt=0.9900, 18 negative triangles
098: dt=0.9900, 11 negative triangles
099: dt=0.9900, 12 negative triangles
100: dt=0.9900, 14 negative triangles
101: dt=0.9900, 12 negative triangles
102: dt=0.9900, 7 negative triangles
103: dt=0.9900, 7 negative triangles
104: dt=0.9900, 5 negative triangles
105: dt=0.9900, 14 negative triangles
106: dt=0.9900, 7 negative triangles
107: dt=0.9900, 6 negative triangles
108: dt=0.9900, 3 negative triangles
109: dt=0.9900, 2 negative triangles
110: dt=0.9900, 5 negative triangles
111: dt=0.9900, 2 negative triangles
112: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 0.0801 hours
FSRUNTIME@ mris_sphere 0.0801 hours 1 threads
#VMPC# mris_sphere VmPeak 537372
mris_sphere done
#--------------------------------------------
#@# Surf Reg lh Fri Jun 13 01:24:48 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_register -curv ../surf/lh.sphere /opt/freesurfer-7.3.2/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg
using smoothwm curvature for final alignment
cwd /tmp/tmps594ishs/freesurfer_output/subjectname/scripts
cmdline mris_register -curv ../surf/lh.sphere /opt/freesurfer-7.3.2/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg
0 inflated.H
1 sulc
2 smoothwm (computed)
7.3.2
7.3.2
reading surface from ../surf/lh.sphere...
reading template parameterization from /opt/freesurfer-7.3.2/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif...
MRISregister() -------
max_passes = 4
min_degrees = 0.500000
max_degrees = 64.000000
nangles = 8
tol=5.0e-01, sigma=0.0, host=fv-az, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height -1.000000
momentum 0.950000
nbhd_size -10
max_nbrs 10
niterations 25
nsurfaces 0
SURFACES 3
flags 16 (10)
use curv 16
no sulc 0
no rigid align 0
mris->nsize 1
mris->hemisphere 0
randomSeed 0
tol=5.0e-01, sigma=0.0, host=fv-az, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
using quadratic fit line minimization
--------------------
1 Reading lh.sulc
tol=1.0e+00, sigma=0.5, host=fv-az, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
curvature mean = 0.000, std = 5.599
curvature mean = 0.040, std = 0.819
curvature mean = 0.012, std = 0.868
Starting MRISrigidBodyAlignGlobal()
Starting new MRISrigidBodyAlignGlobal_findMinSSE()
new MRISrigidBodyAlignGlobal_findMinSSE min @ (4.50, -7.50, -1.50) sse = 149085.1, elapsed since starting=0.2426 min
MRISrigidBodyAlignGlobal() done 0.24 min
curvature mean = 0.014, std = 0.838
curvature mean = 0.003, std = 0.951
curvature mean = 0.009, std = 0.849
curvature mean = 0.002, std = 0.980
curvature mean = 0.008, std = 0.851
curvature mean = 0.000, std = 0.992
2 Reading smoothwm
curvature mean = -0.021, std = 0.245
curvature mean = 0.041, std = 0.250
curvature mean = 0.043, std = 0.401
curvature mean = 0.037, std = 0.308
curvature mean = 0.022, std = 0.605
curvature mean = 0.036, std = 0.336
curvature mean = 0.010, std = 0.742
curvature mean = 0.036, std = 0.348
curvature mean = 0.003, std = 0.838
MRISregister() return, current seed 0
writing registered surface to ../surf/lh.sphere.reg...
-01: dt=0.0000, 0 negative triangles VmPeak 523544
registration took 0.08 hours
#VMPC# mris_register VmPeak 523544
FSRUNTIME@ mris_register 0.0783 hours 1 threads
/tmp/tmps594ishs/freesurfer_output/subjectname/surf /tmp/tmps594ishs/freesurfer_output/subjectname/scripts
ln -sf lh.sphere.reg lh.fsaverage.sphere.reg
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
#--------------------------------------------
#@# Surf Reg rh Fri Jun 13 01:29:30 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_register -curv ../surf/rh.sphere /opt/freesurfer-7.3.2/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg
using smoothwm curvature for final alignment
cwd /tmp/tmps594ishs/freesurfer_output/subjectname/scripts
cmdline mris_register -curv ../surf/rh.sphere /opt/freesurfer-7.3.2/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg
0 inflated.H
1 sulc
2 smoothwm (computed)
7.3.2
7.3.2
reading surface from ../surf/rh.sphere...
reading template parameterization from /opt/freesurfer-7.3.2/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif...
MRISregister() -------
max_passes = 4
min_degrees = 0.500000
max_degrees = 64.000000
nangles = 8
tol=5.0e-01, sigma=0.0, host=fv-az, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height -1.000000
momentum 0.950000
nbhd_size -10
max_nbrs 10
niterations 25
nsurfaces 0
SURFACES 3
flags 16 (10)
use curv 16
no sulc 0
no rigid align 0
mris->nsize 1
mris->hemisphere 1
randomSeed 0
tol=5.0e-01, sigma=0.0, host=fv-az, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000
using quadratic fit line minimization
--------------------
1 Reading rh.sulc
tol=1.0e+00, sigma=0.5, host=fv-az, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
curvature mean = -0.000, std = 5.588
curvature mean = 0.017, std = 0.806
curvature mean = 0.013, std = 0.869
Starting MRISrigidBodyAlignGlobal()
Starting new MRISrigidBodyAlignGlobal_findMinSSE()
new MRISrigidBodyAlignGlobal_findMinSSE min @ (7.00, -5.50, 3.00) sse = 129613.3, elapsed since starting=0.2450 min
MRISrigidBodyAlignGlobal() done 0.25 min
curvature mean = -0.000, std = 0.833
curvature mean = 0.005, std = 0.953
curvature mean = -0.003, std = 0.843
curvature mean = 0.002, std = 0.982
curvature mean = -0.005, std = 0.844
curvature mean = 0.000, std = 0.993
2 Reading smoothwm
curvature mean = -0.022, std = 0.245
curvature mean = 0.033, std = 0.245
curvature mean = 0.049, std = 0.400
curvature mean = 0.031, std = 0.303
curvature mean = 0.023, std = 0.605
curvature mean = 0.029, std = 0.331
curvature mean = 0.011, std = 0.741
curvature mean = 0.029, std = 0.344
curvature mean = 0.003, std = 0.837
MRISregister() return, current seed 0
-01: dt=0.0000, 1 negative triangles VmPeak 522616
096: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 0.07 hours
#VMPC# mris_register VmPeak 522616
FSRUNTIME@ mris_register 0.0749 hours 1 threads
/tmp/tmps594ishs/freesurfer_output/subjectname/surf /tmp/tmps594ishs/freesurfer_output/subjectname/scripts
ln -sf rh.sphere.reg rh.fsaverage.sphere.reg
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
#--------------------------------------------
#@# Jacobian white lh Fri Jun 13 01:34:00 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white
reading surface from ../surf/lh.white.preaparc...
writing curvature file ../surf/lh.jacobian_white
#--------------------------------------------
#@# Jacobian white rh Fri Jun 13 01:34:01 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white
reading surface from ../surf/rh.white.preaparc...
writing curvature file ../surf/rh.jacobian_white
#--------------------------------------------
#@# AvgCurv lh Fri Jun 13 01:34:01 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mrisp_paint -a 5 /opt/freesurfer-7.3.2/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv
averaging curvature patterns 5 times...
reading surface from ../surf/lh.sphere.reg...
reading template parameterization from /opt/freesurfer-7.3.2/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif...
writing curvature file to ../surf/lh.avg_curv...
#--------------------------------------------
#@# AvgCurv rh Fri Jun 13 01:34:02 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mrisp_paint -a 5 /opt/freesurfer-7.3.2/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv
averaging curvature patterns 5 times...
reading surface from ../surf/rh.sphere.reg...
reading template parameterization from /opt/freesurfer-7.3.2/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif...
writing curvature file to ../surf/rh.avg_curv...
#-----------------------------------------
#@# Cortical Parc lh Fri Jun 13 01:34:03 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subjectname lh ../surf/lh.sphere.reg /opt/freesurfer-7.3.2/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot
setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
7.3.2
7.3.2
reading atlas from /opt/freesurfer-7.3.2/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 0.8 using min determinant for regularization = 0.006
0 singular and 342 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1413 labels changed using aseg
relabeling using gibbs priors...
000: 2853 changed, 128612 examined...
001: 655 changed, 11979 examined...
002: 158 changed, 3717 examined...
003: 51 changed, 963 examined...
004: 22 changed, 306 examined...
005: 16 changed, 134 examined...
006: 10 changed, 82 examined...
007: 7 changed, 50 examined...
008: 1 changed, 37 examined...
009: 0 changed, 7 examined...
293 labels changed using aseg
000: 101 total segments, 62 labels (146 vertices) changed
001: 40 total segments, 2 labels (5 vertices) changed
002: 38 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 2 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1741 vertices marked for relabeling...
1741 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 7 seconds.
#-----------------------------------------
#@# Cortical Parc rh Fri Jun 13 01:34:10 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subjectname rh ../surf/rh.sphere.reg /opt/freesurfer-7.3.2/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot
setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
7.3.2
7.3.2
reading atlas from /opt/freesurfer-7.3.2/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 0.7 using min determinant for regularization = 0.004
0 singular and 309 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1235 labels changed using aseg
relabeling using gibbs priors...
000: 2490 changed, 128513 examined...
001: 504 changed, 10872 examined...
002: 98 changed, 3056 examined...
003: 33 changed, 612 examined...
004: 11 changed, 211 examined...
005: 4 changed, 69 examined...
006: 0 changed, 28 examined...
158 labels changed using aseg
000: 95 total segments, 57 labels (192 vertices) changed
001: 42 total segments, 4 labels (4 vertices) changed
002: 37 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 2 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1541 vertices marked for relabeling...
1541 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 7 seconds.
#--------------------------------------------
#@# WhiteSurfs lh Fri Jun 13 01:34:17 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot
7.3.2
7.3.2
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
setenv SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot
Reading in input surface ../surf/lh.white.preaparc
Not smoothing input surface
Area 257220 0.33392 0.10919 0.001133 1.8853
Corner 771660 60.00000 12.77267 0.197116 178.5246
Edge 385830 0.88662 0.18085 0.038419 3.8198
Hinge 385830 8.50431 9.59496 0.000003 179.8698
Reading in aparc ../label/lh.aparc.annot
Reading in input volume brain.finalsurfs.mgz
Reading in wm volume wm.mgz
MRIclipBrightWM(): nthresh=15301, wmmin=5, clip=110
MRIfindBrightNonWM(): 1607 bright non-wm voxels segmented.
Masking bright non-wm for white surface
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
Reading in seg volume aseg.presurf.mgz
Ripping frozen voxels
Ripping vertices not in label ../label/lh.cortex.label
MRISripNotLabel() ripped 8249/128612 vertices (120363 unripped)
Reading in ripping surface ../surf/lh.white.preaparc
Reading in aparc ../label/lh.aparc.annot for ripsurf
Ripping BG
MRISripBasalGanglia(): 1 -2 2 0.5 ripped 342
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247
MRISripSegs(): -2 2 0.5 ripped 0
vertex 64306: xyz = (-31.0111,-10.7648,6.15307) oxyz = (-31.0111,-10.7648,6.15307) wxzy = (-31.0111,-10.7648,6.15307) pxyz = (0,0,0)
CBVO Creating mask 128612
n_averages 4
Iteration 0 =========================================
n_averages=4, current_sigma=2
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000;
border_hi = 111.7148900;
border_low = 71.0000000;
outside_low = 60.4994740;
outside_hi = 111.7148900;
sigma = 2;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128612
Gdiag_no=-1
vno start=0, stop=128612
Replacing 255s with 0s
#SI# sigma=2 had to be increased for 95 vertices, nripped=8591
mean border=81.6, 111 (111) missing vertices, mean dist 0.4 [1.2 (%11.9)->0.7 (%88.1))]
%57 local maxima, %36 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.1934 min
Finding expansion regions
mean absolute distance = 0.74 +- 1.01
2383 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=2.0, host=fv-az, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 100
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0
000: dt: 0.0000, sse=2072407.4, rms=8.883
001: dt: 0.5000, sse=962413.2, rms=5.719 (35.622%)
002: dt: 0.5000, sse=568491.9, rms=4.039 (29.364%)
003: dt: 0.5000, sse=429833.1, rms=3.243 (19.719%)
004: dt: 0.5000, sse=364364.2, rms=2.775 (14.422%)
005: dt: 0.5000, sse=352972.6, rms=2.652 (4.448%)
006: dt: 0.5000, sse=345600.4, rms=2.505 (5.518%)
rms = 2.5449/2.5055, sse=335266.5/345600.4, time step reduction 1 of 3 to 0.250 0 0 1
RMS increased, rejecting step
007: dt: 0.2500, sse=249625.9, rms=1.640 (34.528%)
008: dt: 0.2500, sse=214982.7, rms=1.188 (27.594%)
009: dt: 0.2500, sse=207419.8, rms=1.045 (12.037%)
rms = 0.9977/1.0448, sse=205227.0/207419.8, time step reduction 2 of 3 to 0.125 0 0 1
010: dt: 0.2500, sse=205227.0, rms=0.998 (4.508%)
rms = 0.9545/0.9977, sse=203164.9/205227.0, time step reduction 3 of 3 to 0.062 0 0 1
011: dt: 0.1250, sse=203164.9, rms=0.954 (4.328%)
maximum number of reductions reached, breaking from loop
positioning took 0.8 minutes
Iteration 1 =========================================
n_averages=2, current_sigma=1
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000;
border_hi = 111.7148900;
border_low = 71.0000000;
outside_low = 60.4994740;
outside_hi = 111.7148900;
sigma = 1;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128612
Gdiag_no=-1
vno start=0, stop=128612
Replacing 255s with 0s
#SI# sigma=1 had to be increased for 71 vertices, nripped=8591
mean border=85.4, 131 (55) missing vertices, mean dist -0.3 [0.5 (%74.6)->0.2 (%25.4))]
%73 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.1403 min
Finding expansion regions
mean absolute distance = 0.46 +- 0.71
4157 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=1.0, host=fv-az, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=996559.3, rms=5.781
012: dt: 0.5000, sse=603139.1, rms=4.122 (28.702%)
013: dt: 0.5000, sse=489101.3, rms=3.502 (15.036%)
014: dt: 0.5000, sse=425406.5, rms=3.115 (11.044%)
015: dt: 0.5000, sse=390606.6, rms=2.863 (8.106%)
016: dt: 0.5000, sse=367859.8, rms=2.680 (6.394%)
rms = 2.6585/2.6796, sse=366678.9/367859.8, time step reduction 1 of 3 to 0.250 0 0 1
017: dt: 0.5000, sse=366678.9, rms=2.659 (0.787%)
018: dt: 0.2500, sse=232516.0, rms=1.247 (53.091%)
019: dt: 0.2500, sse=219531.6, rms=1.011 (18.965%)
020: dt: 0.2500, sse=216204.0, rms=0.940 (6.995%)
rms = 0.9181/0.9399, sse=215278.9/216204.0, time step reduction 2 of 3 to 0.125 0 0 1
021: dt: 0.2500, sse=215278.9, rms=0.918 (2.321%)
022: dt: 0.1250, sse=212848.5, rms=0.858 (6.568%)
rms = 0.8562/0.8578, sse=212938.6/212848.5, time step reduction 3 of 3 to 0.062 0 1 1
023: dt: 0.1250, sse=212938.6, rms=0.856 (0.188%)
maximum number of reductions reached, breaking from loop
positioning took 0.8 minutes
Iteration 2 =========================================
n_averages=1, current_sigma=0.5
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000;
border_hi = 111.7148900;
border_low = 71.0000000;
outside_low = 60.4994740;
outside_hi = 111.7148900;
sigma = 0.5;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128612
Gdiag_no=-1
vno start=0, stop=128612
Replacing 255s with 0s
#SI# sigma=0.5 had to be increased for 47 vertices, nripped=8591
mean border=87.8, 97 (36) missing vertices, mean dist -0.2 [0.3 (%73.7)->0.2 (%26.3))]
%82 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0793 min
Finding expansion regions
mean absolute distance = 0.27 +- 0.43
3217 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.5, host=fv-az, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=458879.7, rms=3.364
024: dt: 0.5000, sse=329321.0, rms=2.412 (28.306%)
025: dt: 0.5000, sse=317932.1, rms=2.325 (3.604%)
rms = 2.4057/2.3247, sse=327355.6/317932.1, time step reduction 1 of 3 to 0.250 0 1 1
RMS increased, rejecting step
026: dt: 0.2500, sse=240603.8, rms=1.480 (36.333%)
027: dt: 0.2500, sse=211509.7, rms=0.985 (33.444%)
028: dt: 0.2500, sse=206333.8, rms=0.875 (11.147%)
rms = 0.8449/0.8753, sse=205068.7/206333.8, time step reduction 2 of 3 to 0.125 0 0 1
029: dt: 0.2500, sse=205068.7, rms=0.845 (3.468%)
rms = 0.8101/0.8449, sse=203488.9/205068.7, time step reduction 3 of 3 to 0.062 0 0 1
030: dt: 0.1250, sse=203488.9, rms=0.810 (4.126%)
maximum number of reductions reached, breaking from loop
positioning took 0.5 minutes
Iteration 3 =========================================
n_averages=0, current_sigma=0.25
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000;
border_hi = 111.7148900;
border_low = 71.0000000;
outside_low = 60.4994740;
outside_hi = 111.7148900;
sigma = 0.25;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128612
Gdiag_no=-1
vno start=0, stop=128612
Replacing 255s with 0s
#SI# sigma=0.25 had to be increased for 55 vertices, nripped=8591
mean border=88.5, 108 (29) missing vertices, mean dist -0.0 [0.2 (%57.8)->0.2 (%42.2))]
%85 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0497 min
Finding expansion regions
mean absolute distance = 0.20 +- 0.32
2877 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.2, host=fv-az, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=231820.7, rms=1.401
031: dt: 0.5000, sse=226625.7, rms=1.259 (10.187%)
rms = 1.6344/1.2585, sse=249895.6/226625.7, time step reduction 1 of 3 to 0.250 0 1 1
RMS increased, rejecting step
032: dt: 0.2500, sse=205711.2, rms=0.856 (31.970%)
033: dt: 0.2500, sse=200416.9, rms=0.725 (15.331%)
rms = 0.6942/0.7249, sse=198076.2/200416.9, time step reduction 2 of 3 to 0.125 0 0 1
034: dt: 0.2500, sse=198076.2, rms=0.694 (4.240%)
rms = 0.6706/0.6942, sse=197014.6/198076.2, time step reduction 3 of 3 to 0.062 0 0 1
035: dt: 0.1250, sse=197014.6, rms=0.671 (3.400%)
maximum number of reductions reached, breaking from loop
positioning took 0.4 minutes
Writing output to ../surf/lh.white
#ET# mris_place_surface 2.89 minutes
#VMPC# mris_place_surfaces VmPeak 2091664
mris_place_surface done
#--------------------------------------------
#@# WhiteSurfs rh Fri Jun 13 01:37:16 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot
7.3.2
7.3.2
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
setenv SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot
Reading in input surface ../surf/rh.white.preaparc
Not smoothing input surface
Area 257022 0.33315 0.11032 0.001483 4.1400
Corner 771066 60.00000 12.73578 0.378459 178.6430
Edge 385533 0.88555 0.18084 0.035539 3.9623
Hinge 385533 8.52032 9.62556 0.000028 179.9167
Reading in aparc ../label/rh.aparc.annot
Reading in input volume brain.finalsurfs.mgz
Reading in wm volume wm.mgz
MRIclipBrightWM(): nthresh=15301, wmmin=5, clip=110
MRIfindBrightNonWM(): 1607 bright non-wm voxels segmented.
Masking bright non-wm for white surface
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
Reading in seg volume aseg.presurf.mgz
Ripping frozen voxels
Ripping vertices not in label ../label/rh.cortex.label
MRISripNotLabel() ripped 8261/128513 vertices (120252 unripped)
Reading in ripping surface ../surf/rh.white.preaparc
Reading in aparc ../label/rh.aparc.annot for ripsurf
Ripping BG
MRISripBasalGanglia(): 1 -2 2 0.5 ripped 420
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247
MRISripSegs(): -2 2 0.5 ripped 0
vertex 64257: xyz = (54.7528,-10.1277,35.7877) oxyz = (54.7528,-10.1277,35.7877) wxzy = (54.7528,-10.1277,35.7877) pxyz = (0,0,0)
CBVO Creating mask 128513
n_averages 4
Iteration 0 =========================================
n_averages=4, current_sigma=2
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000;
border_hi = 111.7148900;
border_low = 72.0000000;
outside_low = 61.4994740;
outside_hi = 111.7148900;
sigma = 2;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128513
Gdiag_no=-1
vno start=0, stop=128513
Replacing 255s with 0s
#SI# sigma=2 had to be increased for 99 vertices, nripped=8681
mean border=82.1, 50 (50) missing vertices, mean dist 0.4 [1.3 (%12.3)->0.7 (%87.7))]
%53 local maxima, %40 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.1899 min
Finding expansion regions
mean absolute distance = 0.73 +- 1.02
2505 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=2.0, host=fv-az, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 100
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0
000: dt: 0.0000, sse=1948584.0, rms=8.597
001: dt: 0.5000, sse=911653.1, rms=5.536 (35.601%)
002: dt: 0.5000, sse=547065.5, rms=3.931 (28.999%)
003: dt: 0.5000, sse=420639.8, rms=3.194 (18.747%)
004: dt: 0.5000, sse=363216.7, rms=2.781 (12.919%)
005: dt: 0.5000, sse=350937.6, rms=2.675 (3.823%)
006: dt: 0.5000, sse=334442.5, rms=2.545 (4.862%)
rms = 2.5774/2.5449, sse=339233.1/334442.5, time step reduction 1 of 3 to 0.250 0 1 1
RMS increased, rejecting step
007: dt: 0.2500, sse=247943.9, rms=1.680 (33.985%)
008: dt: 0.2500, sse=217677.9, rms=1.235 (26.485%)
009: dt: 0.2500, sse=209963.8, rms=1.090 (11.706%)
rms = 1.0497/1.0905, sse=208558.8/209963.7, time step reduction 2 of 3 to 0.125 0 0 1
010: dt: 0.2500, sse=208558.8, rms=1.050 (3.737%)
rms = 1.0134/1.0497, sse=207137.4/208558.8, time step reduction 3 of 3 to 0.062 0 0 1
011: dt: 0.1250, sse=207137.4, rms=1.013 (3.460%)
maximum number of reductions reached, breaking from loop
positioning took 0.8 minutes
Iteration 1 =========================================
n_averages=2, current_sigma=1
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000;
border_hi = 111.7148900;
border_low = 72.0000000;
outside_low = 61.4994740;
outside_hi = 111.7148900;
sigma = 1;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128513
Gdiag_no=-1
vno start=0, stop=128513
Replacing 255s with 0s
#SI# sigma=1 had to be increased for 66 vertices, nripped=8681
mean border=85.8, 83 (10) missing vertices, mean dist -0.3 [0.5 (%73.6)->0.2 (%26.4))]
%70 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.1381 min
Finding expansion regions
mean absolute distance = 0.45 +- 0.73
3994 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=1.0, host=fv-az, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=947789.4, rms=5.602
012: dt: 0.5000, sse=582160.6, rms=4.021 (28.223%)
013: dt: 0.5000, sse=472545.2, rms=3.421 (14.915%)
014: dt: 0.5000, sse=416706.6, rms=3.072 (10.217%)
015: dt: 0.5000, sse=384077.9, rms=2.832 (7.800%)
016: dt: 0.5000, sse=362347.1, rms=2.667 (5.815%)
rms = 2.6380/2.6674, sse=360691.7/362347.1, time step reduction 1 of 3 to 0.250 0 0 1
017: dt: 0.5000, sse=360691.7, rms=2.638 (1.101%)
018: dt: 0.2500, sse=229834.1, rms=1.214 (53.984%)
019: dt: 0.2500, sse=216701.5, rms=0.961 (20.853%)
020: dt: 0.2500, sse=212969.7, rms=0.873 (9.130%)
rms = 0.8411/0.8731, sse=211507.6/212969.7, time step reduction 2 of 3 to 0.125 0 0 1
021: dt: 0.2500, sse=211507.6, rms=0.841 (3.666%)
022: dt: 0.1250, sse=209313.7, rms=0.782 (6.979%)
rms = 0.7754/0.7824, sse=208894.7/209313.7, time step reduction 3 of 3 to 0.062 0 0 1
023: dt: 0.1250, sse=208894.7, rms=0.775 (0.896%)
maximum number of reductions reached, breaking from loop
positioning took 0.8 minutes
Iteration 2 =========================================
n_averages=1, current_sigma=0.5
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000;
border_hi = 111.7148900;
border_low = 72.0000000;
outside_low = 61.4994740;
outside_hi = 111.7148900;
sigma = 0.5;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128513
Gdiag_no=-1
vno start=0, stop=128513
Replacing 255s with 0s
#SI# sigma=0.5 had to be increased for 42 vertices, nripped=8681
mean border=88.1, 94 (8) missing vertices, mean dist -0.2 [0.3 (%73.3)->0.2 (%26.7))]
%80 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0771 min
Finding expansion regions
mean absolute distance = 0.27 +- 0.43
2911 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.5, host=fv-az, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=435150.5, rms=3.219
024: dt: 0.5000, sse=313274.4, rms=2.281 (29.145%)
rms = 2.2356/2.2811, sse=306748.5/313274.4, time step reduction 1 of 3 to 0.250 0 0 1
025: dt: 0.5000, sse=306748.5, rms=2.236 (1.994%)
026: dt: 0.2500, sse=212972.1, rms=1.030 (53.912%)
027: dt: 0.2500, sse=204169.2, rms=0.838 (18.689%)
rms = 0.7917/0.8378, sse=202369.2/204169.2, time step reduction 2 of 3 to 0.125 0 0 1
028: dt: 0.2500, sse=202369.2, rms=0.792 (5.504%)
029: dt: 0.1250, sse=200103.3, rms=0.733 (7.473%)
rms = 0.7284/0.7325, sse=199924.0/200103.3, time step reduction 3 of 3 to 0.062 0 0 1
030: dt: 0.1250, sse=199924.0, rms=0.728 (0.567%)
maximum number of reductions reached, breaking from loop
positioning took 0.4 minutes
Iteration 3 =========================================
n_averages=0, current_sigma=0.25
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000;
border_hi = 111.7148900;
border_low = 72.0000000;
outside_low = 61.4994740;
outside_hi = 111.7148900;
sigma = 0.25;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128513
Gdiag_no=-1
vno start=0, stop=128513
Replacing 255s with 0s
#SI# sigma=0.25 had to be increased for 45 vertices, nripped=8681
mean border=88.8, 114 (6) missing vertices, mean dist -0.0 [0.2 (%57.8)->0.2 (%42.2))]
%83 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0485 min
Finding expansion regions
mean absolute distance = 0.20 +- 0.32
2702 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.2, host=fv-az, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=227661.6, rms=1.346
031: dt: 0.5000, sse=222462.8, rms=1.192 (11.475%)
rms = 1.5519/1.1917, sse=241500.2/222462.8, time step reduction 1 of 3 to 0.250 0 1 1
RMS increased, rejecting step
032: dt: 0.2500, sse=200720.6, rms=0.772 (35.190%)
033: dt: 0.2500, sse=194840.4, rms=0.635 (17.821%)
rms = 0.6080/0.6347, sse=194135.0/194840.4, time step reduction 2 of 3 to 0.125 0 0 1
034: dt: 0.2500, sse=194135.0, rms=0.608 (4.205%)
rms = 0.5944/0.6080, sse=192607.9/194135.0, time step reduction 3 of 3 to 0.062 0 0 1
035: dt: 0.1250, sse=192607.9, rms=0.594 (2.238%)
maximum number of reductions reached, breaking from loop
positioning took 0.4 minutes
Writing output to ../surf/rh.white
#ET# mris_place_surface 2.84 minutes
#VMPC# mris_place_surfaces VmPeak 2084600
mris_place_surface done
#--------------------------------------------
#@# T1PialSurf lh Fri Jun 13 01:40:12 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white
7.3.2
7.3.2
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
setenv SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white
Reading in input surface ../surf/lh.white
Not smoothing input surface
Area 257220 0.33538 0.12074 0.000208 2.4830
Corner 771660 60.00000 13.93859 0.041284 178.5246
Edge 385830 0.88960 0.19820 0.015512 3.9128
Hinge 385830 8.54357 9.72700 0.000098 179.9957
Reading white surface coordinates from ../surf/lh.white
Reading repulsion surface coordinates from ../surf/lh.white
Reading in aparc ../label/lh.aparc.annot
Reading in input volume brain.finalsurfs.mgz
Reading in wm volume wm.mgz
MRIclipBrightWM(): nthresh=15301, wmmin=5, clip=110
MRIfindBrightNonWM(): 1607 bright non-wm voxels segmented.
Masking bright non-wm for pial surface mid_gray = 67.8918
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
Reading in seg volume aseg.presurf.mgz
Ripping frozen voxels
Ripping vertices not in label ../label/lh.cortex+hipamyg.label
MRISripNotLabel() ripped 6669/128612 vertices (121943 unripped)
INFO: rip surface needed but not specified, so using input surface
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247
MRISripSegs(): -2 2 0.5 ripped 0
vertex 64306: xyz = (-31.0111,-10.7648,6.15307) oxyz = (-31.0111,-10.7648,6.15307) wxzy = (-31.0111,-10.7648,6.15307) pxyz = (-31.0111,-10.7648,6.15307)
CBVO Creating mask 128612
n_averages 16
Iteration 0 =========================================
n_averages=16, current_sigma=2
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 96.2851100;
border_hi = 60.4994740;
border_low = 39.4984210;
outside_low = 10.0000000;
outside_hi = 55.2492100;
sigma = 2;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 2
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128612
Gdiag_no=-1
vno start=0, stop=128612
Replacing 255s with 0s
#SI# sigma=2 had to be increased for 136 vertices, nripped=6669
mean border=57.7, 117 (117) missing vertices, mean dist 2.2 [1.2 (%0.0)->2.7 (%100.0))]
%19 local maxima, %58 large gradients and %18 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.1572 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=2.0, host=fv-az, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 100
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0
000: dt: 0.0000, sse=24388168.0, rms=31.520
001: dt: 0.5000, sse=17481378.0, rms=26.647 (15.461%)
002: dt: 0.5000, sse=12427076.0, rms=22.418 (15.869%)
003: dt: 0.5000, sse=9038692.0, rms=19.064 (14.961%)
004: dt: 0.5000, sse=6818608.0, rms=16.500 (13.452%)
005: dt: 0.5000, sse=5279241.5, rms=14.456 (12.389%)
006: dt: 0.5000, sse=4122297.5, rms=12.703 (12.123%)
007: dt: 0.5000, sse=3215822.0, rms=11.138 (12.319%)
008: dt: 0.5000, sse=2487525.5, rms=9.699 (12.923%)
009: dt: 0.5000, sse=1907502.6, rms=8.377 (13.631%)
010: dt: 0.5000, sse=1441324.4, rms=7.138 (14.786%)
011: dt: 0.5000, sse=1090044.5, rms=6.039 (15.401%)
012: dt: 0.5000, sse=863133.3, rms=5.206 (13.799%)
013: dt: 0.5000, sse=749018.7, rms=4.730 (9.140%)
014: dt: 0.5000, sse=681625.5, rms=4.423 (6.485%)
015: dt: 0.5000, sse=657704.9, rms=4.307 (2.626%)
016: dt: 0.5000, sse=634997.2, rms=4.193 (2.642%)
rms = 4.1746/4.1931, sse=631841.7/634997.2, time step reduction 1 of 3 to 0.250 0 0 1
017: dt: 0.5000, sse=631841.7, rms=4.175 (0.442%)
018: dt: 0.2500, sse=485639.2, rms=3.360 (19.511%)
019: dt: 0.2500, sse=459525.1, rms=3.193 (4.961%)
rms = 3.1717/3.1934, sse=456560.4/459525.1, time step reduction 2 of 3 to 0.125 0 0 1
020: dt: 0.2500, sse=456560.3, rms=3.172 (0.678%)
021: dt: 0.1250, sse=426729.7, rms=2.969 (6.400%)
rms = 2.9311/2.9687, sse=421501.3/426729.7, time step reduction 3 of 3 to 0.062 0 0 1
022: dt: 0.1250, sse=421501.2, rms=2.931 (1.267%)
maximum number of reductions reached, breaking from loop
positioning took 1.3 minutes
Iteration 1 =========================================
n_averages=8, current_sigma=1
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 96.2851100;
border_hi = 60.4994740;
border_low = 39.4984210;
outside_low = 10.0000000;
outside_hi = 55.2492100;
sigma = 1;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 2
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128612
Gdiag_no=-1
vno start=0, stop=128612
Replacing 255s with 0s
#SI# sigma=1 had to be increased for 3821 vertices, nripped=6669
mean border=55.3, 1057 (26) missing vertices, mean dist 0.2 [0.2 (%43.2)->0.6 (%56.8))]
%38 local maxima, %42 large gradients and %15 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0550 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=1.0, host=fv-az, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=840234.6, rms=4.909
023: dt: 0.5000, sse=701732.8, rms=4.285 (12.720%)
024: dt: 0.5000, sse=662317.2, rms=4.101 (4.293%)
rms = 4.1060/4.1007, sse=664376.3/662317.3, time step reduction 1 of 3 to 0.250 0 1 1
RMS increased, rejecting step
025: dt: 0.2500, sse=532715.1, rms=3.380 (17.567%)
026: dt: 0.2500, sse=485775.9, rms=3.075 (9.021%)
027: dt: 0.2500, sse=474838.8, rms=2.999 (2.469%)
028: dt: 0.2500, sse=466296.0, rms=2.939 (2.027%)
rms = 2.9223/2.9386, sse=464156.7/466296.0, time step reduction 2 of 3 to 0.125 0 0 1
029: dt: 0.2500, sse=464156.7, rms=2.922 (0.554%)
030: dt: 0.1250, sse=435439.0, rms=2.709 (7.288%)
rms = 2.6711/2.7093, sse=430556.1/435439.0, time step reduction 3 of 3 to 0.062 0 0 1
031: dt: 0.1250, sse=430556.2, rms=2.671 (1.413%)
maximum number of reductions reached, breaking from loop
positioning took 0.6 minutes
Iteration 2 =========================================
n_averages=4, current_sigma=0.5
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 96.2851100;
border_hi = 60.4994740;
border_low = 39.4984210;
outside_low = 10.0000000;
outside_hi = 55.2492100;
sigma = 0.5;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 2
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128612
Gdiag_no=-1
vno start=0, stop=128612
Replacing 255s with 0s
#SI# sigma=0.5 had to be increased for 4227 vertices, nripped=6669
mean border=53.3, 1455 (21) missing vertices, mean dist 0.2 [0.2 (%33.4)->0.4 (%66.6))]
%55 local maxima, %24 large gradients and %14 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0318 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.5, host=fv-az, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=640133.9, rms=3.941
rms = 3.8993/3.9414, sse=633741.3/640133.9, time step reduction 1 of 3 to 0.250 0 0 1
032: dt: 0.5000, sse=633741.3, rms=3.899 (1.069%)
033: dt: 0.2500, sse=485563.1, rms=3.023 (22.472%)
034: dt: 0.2500, sse=463115.8, rms=2.866 (5.192%)
rms = 2.8392/2.8661, sse=459482.9/463115.8, time step reduction 2 of 3 to 0.125 0 0 1
035: dt: 0.2500, sse=459482.9, rms=2.839 (0.939%)
036: dt: 0.1250, sse=423298.7, rms=2.561 (9.808%)
rms = 2.5161/2.5607, sse=417829.9/423298.7, time step reduction 3 of 3 to 0.062 0 0 1
037: dt: 0.1250, sse=417829.9, rms=2.516 (1.742%)
maximum number of reductions reached, breaking from loop
positioning took 0.3 minutes
Iteration 3 =========================================
n_averages=2, current_sigma=0.25
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 96.2851100;
border_hi = 60.4994740;
border_low = 39.4984210;
outside_low = 10.0000000;
outside_hi = 55.2492100;
sigma = 0.25;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 2
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128612
Gdiag_no=-1
vno start=0, stop=128612
Replacing 255s with 0s
#SI# sigma=0.25 had to be increased for 3731 vertices, nripped=6669
mean border=52.3, 2284 (20) missing vertices, mean dist 0.1 [0.2 (%37.3)->0.3 (%62.7))]
%63 local maxima, %16 large gradients and %14 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0207 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.2, host=fv-az, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=468110.6, rms=2.899
rms = 3.2588/2.8995, sse=522830.0/468110.6, time step reduction 1 of 3 to 0.250 0 1 1
RMS increased, rejecting step
038: dt: 0.2500, sse=434245.0, rms=2.645 (8.773%)
039: dt: 0.2500, sse=418323.5, rms=2.516 (4.875%)
rms = 2.4909/2.5161, sse=415082.3/418323.5, time step reduction 2 of 3 to 0.125 0 0 1
040: dt: 0.2500, sse=415082.2, rms=2.491 (1.004%)
041: dt: 0.1250, sse=405114.0, rms=2.406 (3.424%)
rms = 2.3796/2.4056, sse=402067.0/405114.0, time step reduction 3 of 3 to 0.062 0 0 1
042: dt: 0.1250, sse=402067.0, rms=2.380 (1.080%)
maximum number of reductions reached, breaking from loop
positioning took 0.3 minutes
Pinning medial wall to white surface
removing intersecting faces
000: 13 intersecting
terminating search with 0 intersecting
Writing output to ../surf/lh.pial.T1
#ET# mris_place_surface 2.93 minutes
#VMPC# mris_place_surfaces VmPeak 1344120
mris_place_surface done
#--------------------------------------------
#@# T1PialSurf rh Fri Jun 13 01:43:14 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white
7.3.2
7.3.2
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
setenv SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white
Reading in input surface ../surf/rh.white
Not smoothing input surface
Area 257022 0.33470 0.12289 0.001255 4.1479
Corner 771066 60.00000 13.89162 0.206599 179.4338
Edge 385533 0.88859 0.19836 0.025653 4.0625
Hinge 385533 8.56625 9.79708 0.000042 179.9721
Reading white surface coordinates from ../surf/rh.white
Reading repulsion surface coordinates from ../surf/rh.white
Reading in aparc ../label/rh.aparc.annot
Reading in input volume brain.finalsurfs.mgz
Reading in wm volume wm.mgz
MRIclipBrightWM(): nthresh=15301, wmmin=5, clip=110
MRIfindBrightNonWM(): 1607 bright non-wm voxels segmented.
Masking bright non-wm for pial surface mid_gray = 68.3918
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
Reading in seg volume aseg.presurf.mgz
Ripping frozen voxels
Ripping vertices not in label ../label/rh.cortex+hipamyg.label
MRISripNotLabel() ripped 6811/128513 vertices (121702 unripped)
INFO: rip surface needed but not specified, so using input surface
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247
MRISripSegs(): -2 2 0.5 ripped 0
vertex 64257: xyz = (54.7828,-10.2038,35.7793) oxyz = (54.7828,-10.2038,35.7793) wxzy = (54.7828,-10.2038,35.7793) pxyz = (54.7828,-10.2038,35.7793)
CBVO Creating mask 128513
n_averages 16
Iteration 0 =========================================
n_averages=16, current_sigma=2
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 96.2851100;
border_hi = 61.4994740;
border_low = 40.4984210;
outside_low = 10.0000000;
outside_hi = 56.2492100;
sigma = 2;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 2
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128513
Gdiag_no=-1
vno start=0, stop=128513
Replacing 255s with 0s
#SI# sigma=2 had to be increased for 138 vertices, nripped=6811
mean border=58.5, 101 (101) missing vertices, mean dist 2.2 [0.6 (%0.0)->2.6 (%100.0))]
%19 local maxima, %59 large gradients and %16 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.1579 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=2.0, host=fv-az, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 100
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0
000: dt: 0.0000, sse=23554578.0, rms=31.002
001: dt: 0.5000, sse=16784692.0, rms=26.130 (15.716%)
002: dt: 0.5000, sse=11834183.0, rms=21.890 (16.226%)
003: dt: 0.5000, sse=8528209.0, rms=18.525 (15.373%)
004: dt: 0.5000, sse=6393952.0, rms=15.979 (13.743%)
005: dt: 0.5000, sse=4940414.5, rms=13.981 (12.505%)
006: dt: 0.5000, sse=3858533.5, rms=12.283 (12.144%)
007: dt: 0.5000, sse=3019278.0, rms=10.782 (12.217%)
008: dt: 0.5000, sse=2353217.5, rms=9.422 (12.619%)
009: dt: 0.5000, sse=1819856.8, rms=8.170 (13.287%)
010: dt: 0.5000, sse=1379682.6, rms=6.969 (14.700%)
011: dt: 0.5000, sse=1049517.1, rms=5.909 (15.202%)
012: dt: 0.5000, sse=830212.5, rms=5.084 (13.973%)
013: dt: 0.5000, sse=719418.8, rms=4.609 (9.337%)
014: dt: 0.5000, sse=660474.6, rms=4.333 (5.981%)
015: dt: 0.5000, sse=640033.5, rms=4.231 (2.363%)
016: dt: 0.5000, sse=620504.2, rms=4.131 (2.369%)
rms = 4.1130/4.1308, sse=617656.1/620504.2, time step reduction 1 of 3 to 0.250 0 0 1
017: dt: 0.5000, sse=617656.1, rms=4.113 (0.432%)
018: dt: 0.2500, sse=473323.8, rms=3.294 (19.917%)
019: dt: 0.2500, sse=446952.4, rms=3.122 (5.230%)
rms = 3.0912/3.1215, sse=442742.5/446952.4, time step reduction 2 of 3 to 0.125 0 0 1
020: dt: 0.2500, sse=442742.5, rms=3.091 (0.971%)
021: dt: 0.1250, sse=415856.7, rms=2.903 (6.076%)
rms = 2.8679/2.9034, sse=411033.0/415856.7, time step reduction 3 of 3 to 0.062 0 0 1
022: dt: 0.1250, sse=411033.0, rms=2.868 (1.222%)
maximum number of reductions reached, breaking from loop
positioning took 1.3 minutes
Iteration 1 =========================================
n_averages=8, current_sigma=1
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 96.2851100;
border_hi = 61.4994740;
border_low = 40.4984210;
outside_low = 10.0000000;
outside_hi = 56.2492100;
sigma = 1;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 2
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128513
Gdiag_no=-1
vno start=0, stop=128513
Replacing 255s with 0s
#SI# sigma=1 had to be increased for 3219 vertices, nripped=6811
mean border=56.0, 919 (26) missing vertices, mean dist 0.2 [0.2 (%42.6)->0.6 (%57.4))]
%39 local maxima, %43 large gradients and %13 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0563 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=1.0, host=fv-az, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=867179.2, rms=5.028
023: dt: 0.5000, sse=699609.2, rms=4.281 (14.848%)
024: dt: 0.5000, sse=654912.9, rms=4.070 (4.926%)
rms = 4.0471/4.0704, sse=651240.2/654912.9, time step reduction 1 of 3 to 0.250 0 0 1
025: dt: 0.5000, sse=651240.2, rms=4.047 (0.573%)
026: dt: 0.2500, sse=485345.0, rms=3.079 (23.914%)
027: dt: 0.2500, sse=454453.8, rms=2.863 (7.028%)
rms = 2.8447/2.8628, sse=452181.8/454453.7, time step reduction 2 of 3 to 0.125 0 0 1
028: dt: 0.2500, sse=452181.8, rms=2.845 (0.634%)
029: dt: 0.1250, sse=422005.4, rms=2.614 (8.124%)
rms = 2.5723/2.6136, sse=416911.5/422005.4, time step reduction 3 of 3 to 0.062 0 0 1
030: dt: 0.1250, sse=416911.5, rms=2.572 (1.579%)
maximum number of reductions reached, breaking from loop
positioning took 0.5 minutes
Iteration 2 =========================================
n_averages=4, current_sigma=0.5
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 96.2851100;
border_hi = 61.4994740;
border_low = 40.4984210;
outside_low = 10.0000000;
outside_hi = 56.2492100;
sigma = 0.5;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 2
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128513
Gdiag_no=-1
vno start=0, stop=128513
Replacing 255s with 0s
#SI# sigma=0.5 had to be increased for 3654 vertices, nripped=6811
mean border=53.9, 1203 (23) missing vertices, mean dist 0.2 [0.2 (%33.3)->0.4 (%66.7))]
%56 local maxima, %25 large gradients and %13 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0331 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.5, host=fv-az, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=644639.2, rms=3.971
031: dt: 0.5000, sse=625780.6, rms=3.862 (2.733%)
rms = 3.9240/3.8623, sse=634568.0/625780.6, time step reduction 1 of 3 to 0.250 0 1 1
RMS increased, rejecting step
032: dt: 0.2500, sse=494187.5, rms=3.082 (20.195%)
033: dt: 0.2500, sse=450274.9, rms=2.777 (9.903%)
034: dt: 0.2500, sse=443713.7, rms=2.727 (1.812%)
rms = 2.6917/2.7268, sse=438959.9/443713.7, time step reduction 2 of 3 to 0.125 0 0 1
035: dt: 0.2500, sse=438959.9, rms=2.692 (1.286%)
036: dt: 0.1250, sse=412416.7, rms=2.477 (7.984%)
rms = 2.4375/2.4768, sse=407744.0/412416.7, time step reduction 3 of 3 to 0.062 0 0 1
037: dt: 0.1250, sse=407744.0, rms=2.437 (1.589%)
maximum number of reductions reached, breaking from loop
positioning took 0.5 minutes
Iteration 3 =========================================
n_averages=2, current_sigma=0.25
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 96.2851100;
border_hi = 61.4994740;
border_low = 40.4984210;
outside_low = 10.0000000;
outside_hi = 56.2492100;
sigma = 0.25;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 2
thresh = 0
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=128513
Gdiag_no=-1
vno start=0, stop=128513
Replacing 255s with 0s
#SI# sigma=0.25 had to be increased for 3388 vertices, nripped=6811
mean border=52.8, 1833 (20) missing vertices, mean dist 0.1 [0.2 (%36.5)->0.3 (%63.5))]
%65 local maxima, %16 large gradients and %13 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0215 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning pial surface
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->check_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.2, host=fv-az, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=461868.7, rms=2.861
rms = 3.1951/2.8609, sse=512028.5/461868.7, time step reduction 1 of 3 to 0.250 0 1 1
RMS increased, rejecting step
038: dt: 0.2500, sse=425401.6, rms=2.581 (9.771%)
039: dt: 0.2500, sse=407793.3, rms=2.434 (5.710%)
rms = 2.4111/2.4340, sse=404976.3/407793.3, time step reduction 2 of 3 to 0.125 0 0 1
040: dt: 0.2500, sse=404976.3, rms=2.411 (0.939%)
041: dt: 0.1250, sse=395850.5, rms=2.330 (3.359%)
rms = 2.3102/2.3301, sse=393576.2/395850.5, time step reduction 3 of 3 to 0.062 0 0 1
042: dt: 0.1250, sse=393576.2, rms=2.310 (0.856%)
maximum number of reductions reached, breaking from loop
positioning took 0.3 minutes
Pinning medial wall to white surface
removing intersecting faces
000: 6 intersecting
001: 4 intersecting
terminating search with 0 intersecting
Writing output to ../surf/rh.pial.T1
#ET# mris_place_surface 2.94 minutes
#VMPC# mris_place_surfaces VmPeak 1342884
mris_place_surface done
#@# white curv lh Fri Jun 13 01:46:16 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
insurf ../surf/lh.white, nbrs 2, curvature_avgs 10
writing curvature file ../surf/lh.curv
#@# white area lh Fri Jun 13 01:46:17 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
writing curvature file ../surf/lh.area
#@# pial curv lh Fri Jun 13 01:46:18 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
insurf ../surf/lh.pial, nbrs 2, curvature_avgs 10
writing curvature file ../surf/lh.curv.pial
#@# pial area lh Fri Jun 13 01:46:19 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
writing curvature file ../surf/lh.area.pial
#@# thickness lh Fri Jun 13 01:46:20 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness
0 of 128612 vertices processed
25000 of 128612 vertices processed
50000 of 128612 vertices processed
75000 of 128612 vertices processed
100000 of 128612 vertices processed
125000 of 128612 vertices processed
0 of 128612 vertices processed
25000 of 128612 vertices processed
50000 of 128612 vertices processed
75000 of 128612 vertices processed
100000 of 128612 vertices processed
125000 of 128612 vertices processed
thickness calculation complete, 447:866 truncations.
69781 vertices at 0 distance
113802 vertices at 1 distance
48119 vertices at 2 distance
16413 vertices at 3 distance
5678 vertices at 4 distance
2011 vertices at 5 distance
705 vertices at 6 distance
254 vertices at 7 distance
123 vertices at 8 distance
88 vertices at 9 distance
33 vertices at 10 distance
31 vertices at 11 distance
27 vertices at 12 distance
34 vertices at 13 distance
36 vertices at 14 distance
35 vertices at 15 distance
13 vertices at 16 distance
9 vertices at 17 distance
7 vertices at 18 distance
10 vertices at 19 distance
15 vertices at 20 distance
writing curvature file ../surf/lh.thickness
#@# area and vertex vol lh Fri Jun 13 01:46:40 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness
/tmp/tmps594ishs/freesurfer_output/subjectname/surf
mris_calc -o lh.area.mid lh.area add lh.area.pial
Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
mris_calc -o lh.area.mid lh.area.mid div 2
Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ]
mris_convert --volume subjectname lh /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.volume
masking with /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.cortex.label
Total face volume 237631
Total vertex volume 237412 (mask=0)
#@# subjectname lh 237412
vertexvol Done
#@# white curv rh Fri Jun 13 01:46:41 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
insurf ../surf/rh.white, nbrs 2, curvature_avgs 10
writing curvature file ../surf/rh.curv
#@# white area rh Fri Jun 13 01:46:43 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
writing curvature file ../surf/rh.area
#@# pial curv rh Fri Jun 13 01:46:43 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial
insurf ../surf/rh.pial, nbrs 2, curvature_avgs 10
writing curvature file ../surf/rh.curv.pial
#@# pial area rh Fri Jun 13 01:46:45 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial
writing curvature file ../surf/rh.area.pial
#@# thickness rh Fri Jun 13 01:46:46 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness
0 of 128513 vertices processed
25000 of 128513 vertices processed
50000 of 128513 vertices processed
75000 of 128513 vertices processed
100000 of 128513 vertices processed
125000 of 128513 vertices processed
0 of 128513 vertices processed
25000 of 128513 vertices processed
50000 of 128513 vertices processed
75000 of 128513 vertices processed
100000 of 128513 vertices processed
125000 of 128513 vertices processed
thickness calculation complete, 340:911 truncations.
71724 vertices at 0 distance
113808 vertices at 1 distance
47037 vertices at 2 distance
15757 vertices at 3 distance
5355 vertices at 4 distance
1937 vertices at 5 distance
654 vertices at 6 distance
285 vertices at 7 distance
125 vertices at 8 distance
74 vertices at 9 distance
48 vertices at 10 distance
29 vertices at 11 distance
14 vertices at 12 distance
29 vertices at 13 distance
29 vertices at 14 distance
22 vertices at 15 distance
23 vertices at 16 distance
17 vertices at 17 distance
22 vertices at 18 distance
20 vertices at 19 distance
17 vertices at 20 distance
writing curvature file ../surf/rh.thickness
#@# area and vertex vol rh Fri Jun 13 01:47:06 UTC 2025
cd /tmp/tmps594ishs/freesurfer_output/subjectname/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness
/tmp/tmps594ishs/freesurfer_output/subjectname/surf
mris_calc -o rh.area.mid rh.area add rh.area.pial
Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
mris_calc -o rh.area.mid rh.area.mid div 2
Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ]
mris_convert --volume subjectname rh /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.volume
masking with /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.cortex.label
Total face volume 234693
Total vertex volume 234487 (mask=0)
#@# subjectname rh 234487
vertexvol Done
#-----------------------------------------
#@# Curvature Stats lh Fri Jun 13 01:47:07 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/surf
mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm subjectname lh curv sulc
Toggling save flag on curvature files [ ok ]
Outputting results using filestem [ ../stats/lh.curv.stats ]
Toggling save flag on curvature files [ ok ]
Setting surface [ subjectname/lh.smoothwm ]
Reading surface...
[ ok ]
Setting texture [ curv ]
Reading texture... [ ok ]
Setting texture [ sulc ]
Reading texture...Gb_filter = 0
[ ok ]
Calculating Discrete Principal Curvatures...
Determining geometric order for vno faces... [###
########
#########] [ ok ]
Determining KH curvatures... [#
#
#
#
#
##
#
#
#
#
##
#
#
#
#
##
#] [ ok ]
Determining k1k2 curvatures... [####################] [ ok ]
deltaViolations [ 193 ]
Gb_filter = 0
WARN: S lookup min: -0.316698
WARN: S explicit min: 0.000000 vertex = 145
#-----------------------------------------
#@# Curvature Stats rh Fri Jun 13 01:47:08 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/surf
mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm subjectname rh curv sulc
Toggling save flag on curvature files [ ok ]
Outputting results using filestem [ ../stats/rh.curv.stats ]
Toggling save flag on curvature files [ ok ]
Setting surface [ subjectname/rh.smoothwm ]
Reading surface...
[ ok ]
Setting texture [ curv ]
Reading texture... [ ok ]
Setting texture [ sulc ]
Reading texture...Gb_filter = 0
[ ok ]
Calculating Discrete Principal Curvatures...
Determining geometric order for vno faces... [#
#########
#########
#] [ ok ]
Determining KH curvatures... [
##
#
#
#
#
##
#
#
#
#
##
#
#
#
#
##] [ ok ]
Determining k1k2 curvatures... [####################] [ ok ]
deltaViolations [ 198 ]
Gb_filter = 0
WARN: S lookup min: -0.251083
WARN: S explicit min: 0.000000 vertex = 14
#--------------------------------------------
#@# Cortical ribbon mask Fri Jun 13 01:47:10 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/mri
mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon subjectname
SUBJECTS_DIR is /tmp/tmps594ishs/freesurfer_output
loading input data...
Running hemis serially
Processing left hemi
computing distance to left white surface
computing distance to left pial surface
Processing right hemi
computing distance to right white surface
computing distance to right pial surface
hemi masks overlap voxels = 135
writing volume /tmp/tmps594ishs/freesurfer_output/subjectname/mri/ribbon.mgz
mris_volmask took 4.14 minutes
writing ribbon files
#-----------------------------------------
#@# Cortical Parc 2 lh Fri Jun 13 01:51:19 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subjectname lh ../surf/lh.sphere.reg /opt/freesurfer-7.3.2/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot
setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
7.3.2
7.3.2
reading atlas from /opt/freesurfer-7.3.2/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 3.0 using min determinant for regularization = 0.088
0 singular and 0 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
14 labels changed using aseg
relabeling using gibbs priors...
000: 8279 changed, 128612 examined...
001: 1871 changed, 32219 examined...
002: 557 changed, 10125 examined...
003: 233 changed, 3234 examined...
004: 104 changed, 1396 examined...
005: 37 changed, 617 examined...
006: 12 changed, 230 examined...
007: 7 changed, 74 examined...
008: 4 changed, 41 examined...
009: 3 changed, 21 examined...
010: 4 changed, 17 examined...
011: 3 changed, 14 examined...
012: 0 changed, 18 examined...
4 labels changed using aseg
000: 208 total segments, 123 labels (1279 vertices) changed
001: 93 total segments, 8 labels (43 vertices) changed
002: 85 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 32 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1185 vertices marked for relabeling...
1185 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 10 seconds.
#-----------------------------------------
#@# Cortical Parc 2 rh Fri Jun 13 01:51:29 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subjectname rh ../surf/rh.sphere.reg /opt/freesurfer-7.3.2/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot
setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
7.3.2
7.3.2
reading atlas from /opt/freesurfer-7.3.2/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 1.4 using min determinant for regularization = 0.021
0 singular and 0 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
4 labels changed using aseg
relabeling using gibbs priors...
000: 8192 changed, 128513 examined...
001: 1769 changed, 32291 examined...
002: 492 changed, 9628 examined...
003: 181 changed, 2814 examined...
004: 90 changed, 1044 examined...
005: 40 changed, 513 examined...
006: 27 changed, 230 examined...
007: 12 changed, 134 examined...
008: 5 changed, 74 examined...
009: 1 changed, 37 examined...
010: 1 changed, 7 examined...
011: 0 changed, 6 examined...
2 labels changed using aseg
000: 204 total segments, 119 labels (1461 vertices) changed
001: 87 total segments, 2 labels (3 vertices) changed
002: 85 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 17 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1138 vertices marked for relabeling...
1138 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 10 seconds.
#-----------------------------------------
#@# Cortical Parc 3 lh Fri Jun 13 01:51:39 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subjectname lh ../surf/lh.sphere.reg /opt/freesurfer-7.3.2/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot
setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
7.3.2
7.3.2
reading atlas from /opt/freesurfer-7.3.2/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 1.4 using min determinant for regularization = 0.020
0 singular and 383 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1660 labels changed using aseg
relabeling using gibbs priors...
000: 1829 changed, 128612 examined...
001: 428 changed, 8651 examined...
002: 127 changed, 2411 examined...
003: 49 changed, 750 examined...
004: 27 changed, 285 examined...
005: 22 changed, 153 examined...
006: 12 changed, 112 examined...
007: 11 changed, 75 examined...
008: 11 changed, 52 examined...
009: 7 changed, 56 examined...
010: 7 changed, 44 examined...
011: 1 changed, 29 examined...
012: 0 changed, 7 examined...
256 labels changed using aseg
000: 44 total segments, 11 labels (128 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 1 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
928 vertices marked for relabeling...
928 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 7 seconds.
#-----------------------------------------
#@# Cortical Parc 3 rh Fri Jun 13 01:51:46 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 subjectname rh ../surf/rh.sphere.reg /opt/freesurfer-7.3.2/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot
setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
7.3.2
7.3.2
reading atlas from /opt/freesurfer-7.3.2/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 0.9 using min determinant for regularization = 0.009
0 singular and 325 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1812 labels changed using aseg
relabeling using gibbs priors...
000: 1850 changed, 128513 examined...
001: 407 changed, 8622 examined...
002: 138 changed, 2375 examined...
003: 52 changed, 843 examined...
004: 22 changed, 285 examined...
005: 8 changed, 126 examined...
006: 7 changed, 54 examined...
007: 8 changed, 40 examined...
008: 7 changed, 40 examined...
009: 8 changed, 38 examined...
010: 6 changed, 41 examined...
011: 3 changed, 33 examined...
012: 5 changed, 20 examined...
013: 4 changed, 17 examined...
014: 6 changed, 22 examined...
015: 2 changed, 25 examined...
016: 3 changed, 12 examined...
017: 4 changed, 16 examined...
018: 6 changed, 18 examined...
019: 4 changed, 25 examined...
020: 3 changed, 22 examined...
021: 3 changed, 14 examined...
022: 4 changed, 17 examined...
023: 3 changed, 16 examined...
024: 3 changed, 17 examined...
025: 2 changed, 18 examined...
026: 2 changed, 15 examined...
027: 0 changed, 13 examined...
308 labels changed using aseg
000: 43 total segments, 10 labels (57 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 8 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
906 vertices marked for relabeling...
906 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 7 seconds.
#-----------------------------------------
#@# WM/GM Contrast lh Fri Jun 13 01:51:54 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
pctsurfcon --s subjectname --lh-only
Log file is /tmp/tmps594ishs/freesurfer_output/subjectname/scripts/pctsurfcon.log
Fri Jun 13 01:51:54 UTC 2025
setenv SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
cd /tmp/tmps594ishs/freesurfer_output/subjectname/scripts
/opt/freesurfer-7.3.2/bin/pctsurfcon
pctsurfcon 7.3.2
Linux fv-az1121-699 6.8.0-1029-azure #34~22.04.1-Ubuntu SMP Thu May 1 02:51:54 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /opt/freesurfer-7.3.2
mri_vol2surf --mov /tmp/tmps594ishs/freesurfer_output/subjectname/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /tmp/tmps594ishs/freesurfer_output/subjectname/surf/tmp.pctsurfcon.12768/lh.wm.mgh --regheader subjectname --cortex
srcvol = /tmp/tmps594ishs/freesurfer_output/subjectname/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjDist = -1
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
Using /tmp/tmps594ishs/freesurfer_output/subjectname/mri/orig.mgz as target reference.
-------- original matrix -----------
-1.00000 0.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 -0.00002;
0.00000 -1.00000 0.00000 0.00001;
0.00000 0.00000 0.00000 1.00000;
-------- original matrix -----------
Loading label /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.cortex.label
Reading surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
Projecting -1 -1 1
1 -1 -1 -1
using old
Done mapping volume to surface
Number of source voxels hit = 124298
Masking with /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.cortex.label
Writing to /tmp/tmps594ishs/freesurfer_output/subjectname/surf/tmp.pctsurfcon.12768/lh.wm.mgh
Dim: 128612 1 1
mri_vol2surf --mov /tmp/tmps594ishs/freesurfer_output/subjectname/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /tmp/tmps594ishs/freesurfer_output/subjectname/surf/tmp.pctsurfcon.12768/lh.gm.mgh --projfrac 0.3 --regheader subjectname --cortex
srcvol = /tmp/tmps594ishs/freesurfer_output/subjectname/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.3
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
Using /tmp/tmps594ishs/freesurfer_output/subjectname/mri/orig.mgz as target reference.
-------- original matrix -----------
-1.00000 0.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 -0.00002;
0.00000 -1.00000 0.00000 0.00001;
0.00000 0.00000 0.00000 1.00000;
-------- original matrix -----------
Loading label /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.cortex.label
Reading surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Done reading source surface
Reading thickness /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.thickness
Done
Mapping Source Volume onto Source Subject Surface
Projecting 0.3 0.3 1
1 0.3 0.3 0.3
using old
Done mapping volume to surface
Number of source voxels hit = 128359
Masking with /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.cortex.label
Writing to /tmp/tmps594ishs/freesurfer_output/subjectname/surf/tmp.pctsurfcon.12768/lh.gm.mgh
Dim: 128612 1 1
mri_concat /tmp/tmps594ishs/freesurfer_output/subjectname/surf/tmp.pctsurfcon.12768/lh.wm.mgh /tmp/tmps594ishs/freesurfer_output/subjectname/surf/tmp.pctsurfcon.12768/lh.gm.mgh --paired-diff-norm --mul 100 --o /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.w-g.pct.mgh
ninputs = 2
Checking inputs
nframestot = 2
Allocing output
Done allocing
Combining pairs
nframes = 1
Multiplying by 100.000000
Writing to /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.w-g.pct.mgh
mri_segstats --in /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.w-g.pct.mgh --annot subjectname lh aparc --sum /tmp/tmps594ishs/freesurfer_output/subjectname/stats/lh.w-g.pct.stats --snr
7.3.2
cwd
cmdline mri_segstats --in /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.w-g.pct.mgh --annot subjectname lh aparc --sum /tmp/tmps594ishs/freesurfer_output/subjectname/stats/lh.w-g.pct.stats --snr
sysname Linux
hostname fv-az1121-699
machine x86_64
user runner
whitesurfname white
UseRobust 0
Constructing seg from annotation
Reading annotation /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.aparc.annot
Seg base 1000
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.w-g.pct.mgh
Vertex Area is 0.670758 mm^3
Generating list of segmentation ids
Found 36 segmentations
Computing statistics for each segmentation
Reporting on 35 segmentations
Using PrintSegStat
mri_segstats done
Cleaning up
#-----------------------------------------
#@# WM/GM Contrast rh Fri Jun 13 01:52:21 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
pctsurfcon --s subjectname --rh-only
Log file is /tmp/tmps594ishs/freesurfer_output/subjectname/scripts/pctsurfcon.log
Fri Jun 13 01:52:21 UTC 2025
setenv SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
cd /tmp/tmps594ishs/freesurfer_output/subjectname/scripts
/opt/freesurfer-7.3.2/bin/pctsurfcon
pctsurfcon 7.3.2
Linux fv-az1121-699 6.8.0-1029-azure #34~22.04.1-Ubuntu SMP Thu May 1 02:51:54 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /opt/freesurfer-7.3.2
mri_vol2surf --mov /tmp/tmps594ishs/freesurfer_output/subjectname/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /tmp/tmps594ishs/freesurfer_output/subjectname/surf/tmp.pctsurfcon.12833/rh.wm.mgh --regheader subjectname --cortex
srcvol = /tmp/tmps594ishs/freesurfer_output/subjectname/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
ProjDist = -1
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
Using /tmp/tmps594ishs/freesurfer_output/subjectname/mri/orig.mgz as target reference.
-------- original matrix -----------
-1.00000 0.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 -0.00002;
0.00000 -1.00000 0.00000 0.00001;
0.00000 0.00000 0.00000 1.00000;
-------- original matrix -----------
Loading label /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.cortex.label
Reading surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
Projecting -1 -1 1
1 -1 -1 -1
using old
Done mapping volume to surface
Number of source voxels hit = 124108
Masking with /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.cortex.label
Writing to /tmp/tmps594ishs/freesurfer_output/subjectname/surf/tmp.pctsurfcon.12833/rh.wm.mgh
Dim: 128513 1 1
mri_vol2surf --mov /tmp/tmps594ishs/freesurfer_output/subjectname/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /tmp/tmps594ishs/freesurfer_output/subjectname/surf/tmp.pctsurfcon.12833/rh.gm.mgh --projfrac 0.3 --regheader subjectname --cortex
srcvol = /tmp/tmps594ishs/freesurfer_output/subjectname/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
ProjFrac = 0.3
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
Using /tmp/tmps594ishs/freesurfer_output/subjectname/mri/orig.mgz as target reference.
-------- original matrix -----------
-1.00000 0.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 -0.00002;
0.00000 -1.00000 0.00000 0.00001;
0.00000 0.00000 0.00000 1.00000;
-------- original matrix -----------
Loading label /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.cortex.label
Reading surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Done reading source surface
Reading thickness /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.thickness
Done
Mapping Source Volume onto Source Subject Surface
Projecting 0.3 0.3 1
1 0.3 0.3 0.3
using old
Done mapping volume to surface
Number of source voxels hit = 128248
Masking with /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.cortex.label
Writing to /tmp/tmps594ishs/freesurfer_output/subjectname/surf/tmp.pctsurfcon.12833/rh.gm.mgh
Dim: 128513 1 1
mri_concat /tmp/tmps594ishs/freesurfer_output/subjectname/surf/tmp.pctsurfcon.12833/rh.wm.mgh /tmp/tmps594ishs/freesurfer_output/subjectname/surf/tmp.pctsurfcon.12833/rh.gm.mgh --paired-diff-norm --mul 100 --o /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.w-g.pct.mgh
ninputs = 2
Checking inputs
nframestot = 2
Allocing output
Done allocing
Combining pairs
nframes = 1
Multiplying by 100.000000
Writing to /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.w-g.pct.mgh
mri_segstats --in /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.w-g.pct.mgh --annot subjectname rh aparc --sum /tmp/tmps594ishs/freesurfer_output/subjectname/stats/rh.w-g.pct.stats --snr
7.3.2
cwd
cmdline mri_segstats --in /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.w-g.pct.mgh --annot subjectname rh aparc --sum /tmp/tmps594ishs/freesurfer_output/subjectname/stats/rh.w-g.pct.stats --snr
sysname Linux
hostname fv-az1121-699
machine x86_64
user runner
whitesurfname white
UseRobust 0
Constructing seg from annotation
Reading annotation /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.aparc.annot
Seg base 2000
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.w-g.pct.mgh
Vertex Area is 0.669383 mm^3
Generating list of segmentation ids
Found 36 segmentations
Computing statistics for each segmentation
Reporting on 35 segmentations
Using PrintSegStat
mri_segstats done
Cleaning up
#-----------------------------------------
#@# Relabel Hypointensities Fri Jun 13 01:52:48 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/mri
mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz
reading input surface ../surf/lh.white...
relabeling lh hypointensities...
1750 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
1556 voxels changed to hypointensity...
3280 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# APas-to-ASeg Fri Jun 13 01:52:58 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/mri
mri_surf2volseg --o aseg.mgz --i aseg.presurf.hypos.mgz --fix-presurf-with-ribbon /tmp/tmps594ishs/freesurfer_output/subjectname/mri/ribbon.mgz --threads 1 --lh-cortex-mask /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.cortex.label --lh-white /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white --lh-pial /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.pial --rh-cortex-mask /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.cortex.label --rh-white /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white --rh-pial /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.pial
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
outvol aseg.mgz
4 avail.processors, using 1
Loading aseg.presurf.hypos.mgz
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/mri/ribbon.mgz
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.pial
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.cortex.label
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.pial
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.cortex.label
Done loading
0
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
20
21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39
40 41 42
43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
60 61 62 63
64 65 66
67 68 69 70 71
72 73
74 75
76 77
78 79
80 81
82 83
84 85
86 87
88
89 90
91
92 93
94 95
96 97
98 99
100
101 102
103 104
105 106
107 108 109
110 111
112 113
114 115
116
117 118
119
120
121 122
123 124
125 126
127
128
129
130
131 132
133 134
135 136
137
138 139
140 141
142 143
144 145
146 147 148
149 150
151 152
153 154
155 156 157
158 159
160 161 162
163 164
165 166
167
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170
171 172
173 174
175 176
177 178
179
180
181 182 183
184 185 186 187
188 189 190 191 192
193 194 195 196 197 198 199
200 201 202 203 204 205 206 207
208 209 210 211 212 213 214 215 216 217 218 219
220 221 222 223 224 225 226 227
228 229 230 231 232 233 234 235 236 237 238 239
240 241 242 243 244 245 246 247
248 249 250 251 252 253 254 255
nrelabeled = 127981
ndotcheck = 0
Starting Surf2VolSeg free
free done
#VMPC# mri_surf2volseg VmPeak 902320
mri_surf2volseg done
mri_brainvol_stats subjectname
ComputeBrainVolumeStats2 VoxelVol=1, KeepCSF=1
#CBVS2 MaskVol 1603823.0
#CBVS2 BrainSegVol 1140905.0
#CBVS2 BrainSegVolNotVent 1120478.0
#CBVS2 SupraTentVol 1021007.0
#CBVS2 SupraTentVolNotVent 1000580.0
#CBVS2 lhCtxGM 237908.9
#CBVS2 rhCtxGM 234976.8
#CBVS2 lhCerebralWM 237319.5
#CBVS2 rhCerebralWM 234735.5
#CBVS2 SubCortGMVol 55919.0
#CBVS2 CerebellumVol 119898.0
#CBVS2 CerebellumGMVol 91121.0
#CBVS2 VentChorVol 17009.0
#CBVS2 3rd4th5thCSF 3418.0
#CBVS2 AllCSF 20427.0
#CBVS2 CCVol 4197.0
#-----------------------------------------
#@# AParc-to-ASeg aparc Fri Jun 13 01:53:09 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/mri
mri_surf2volseg --o aparc+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.aparc.annot 1000 --lh-cortex-mask /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.cortex.label --lh-white /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white --lh-pial /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.pial --rh-annot /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.aparc.annot 2000 --rh-cortex-mask /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.cortex.label --rh-white /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white --rh-pial /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.pial
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
outvol aparc+aseg.mgz
4 avail.processors, using 1
Loading aseg.mgz
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.pial
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.cortex.label
Ripping lh vertices labeled not in lh.cortex.label
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Loading /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.aparc.annot
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.pial
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.cortex.label
Ripping rh vertices labeled not in rh.cortex.label
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Loading /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.aparc.annot
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Starting Surf2VolSeg free
free done
#VMPC# mri_surf2volseg VmPeak 886468
mri_surf2volseg done
#-----------------------------------------
#@# AParc-to-ASeg aparc.a2009s Fri Jun 13 01:54:02 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/mri
mri_surf2volseg --o aparc.a2009s+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.aparc.a2009s.annot 11100 --lh-cortex-mask /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.cortex.label --lh-white /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white --lh-pial /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.pial --rh-annot /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.aparc.a2009s.annot 12100 --rh-cortex-mask /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.cortex.label --rh-white /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white --rh-pial /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.pial
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
outvol aparc.a2009s+aseg.mgz
4 avail.processors, using 1
Loading aseg.mgz
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.pial
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.cortex.label
Ripping lh vertices labeled not in lh.cortex.label
ripped 8249 vertices from lh hemi
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.aparc.a2009s.annot
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.pial
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.cortex.label
Ripping rh vertices labeled not in rh.cortex.label
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Loading /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.aparc.a2009s.annot
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#VMPC# mri_surf2volseg VmPeak 886564
mri_surf2volseg done
#-----------------------------------------
#@# AParc-to-ASeg aparc.DKTatlas Fri Jun 13 01:54:55 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/mri
mri_surf2volseg --o aparc.DKTatlas+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.aparc.DKTatlas.annot 1000 --lh-cortex-mask /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.cortex.label --lh-white /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white --lh-pial /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.pial --rh-annot /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.aparc.DKTatlas.annot 2000 --rh-cortex-mask /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.cortex.label --rh-white /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white --rh-pial /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.pial
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
outvol aparc.DKTatlas+aseg.mgz
4 avail.processors, using 1
Loading aseg.mgz
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.pial
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.cortex.label
Ripping lh vertices labeled not in lh.cortex.label
ripped 8249 vertices from lh hemi
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.aparc.DKTatlas.annot
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.pial
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.cortex.label
Ripping rh vertices labeled not in rh.cortex.label
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Loading /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.aparc.DKTatlas.annot
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Starting Surf2VolSeg free
free done
#VMPC# mri_surf2volseg VmPeak 886464
mri_surf2volseg done
#-----------------------------------------
#@# WMParc Fri Jun 13 01:55:48 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/mri
mri_surf2volseg --o wmparc.mgz --label-wm --i aparc+aseg.mgz --threads 1 --lh-annot /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.aparc.annot 3000 --lh-cortex-mask /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.cortex.label --lh-white /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white --lh-pial /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.pial --rh-annot /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.aparc.annot 4000 --rh-cortex-mask /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.cortex.label --rh-white /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white --rh-pial /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.pial
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
outvol wmparc.mgz
4 avail.processors, using 1
Loading aparc+aseg.mgz
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.pial
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.cortex.label
Ripping lh vertices labeled not in lh.cortex.label
ripped 8249 vertices from lh hemi
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.aparc.annot
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.pial
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.cortex.label
Ripping rh vertices labeled not in rh.cortex.label
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Loading /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.aparc.annot
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Starting Surf2VolSeg free
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#VMPC# mri_surf2volseg VmPeak 886468
mri_surf2volseg done
mri_segstats --seed 1234 --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subjectname --surf-wm-vol --ctab /opt/freesurfer-7.3.2/WMParcStatsLUT.txt --etiv
setting seed for random number genererator to 1234
7.3.2
cwd
cmdline mri_segstats --seed 1234 --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subjectname --surf-wm-vol --ctab /opt/freesurfer-7.3.2/WMParcStatsLUT.txt --etiv
sysname Linux
hostname fv-az1121-699
machine x86_64
user runner
whitesurfname white
UseRobust 0
atlas_icv (eTIV) = 1414190 mm^3 (det: 1.377541 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
Loading mri/norm.mgz
Loading mri/norm.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 390 segmentations
Computing statistics for each segmentation
Reporting on 70 segmentations
Using PrintSegStat
mri_segstats done
#-----------------------------------------
#@# Parcellation Stats lh Fri Jun 13 01:59:25 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subjectname lh white
computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /tmp/tmps594ishs/freesurfer_output/subjectname/mri/wm.mgz...
reading input surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white...
reading input pial surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.pial...
reading input white surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 237631
Total vertex volume 237412 (mask=0)
Saving annotation colortable ../label/aparc.annot.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1414190 mm^3 (det: 1.377541 )
1461 956 2159 2.484 0.502 0.078 0.010 5 0.7 bankssts
1060 689 1599 2.141 0.650 0.121 0.014 12 0.8 caudalanteriorcingulate
3468 2242 7254 2.998 0.624 0.102 0.019 24 2.7 caudalmiddlefrontal
2446 1700 4110 2.266 0.667 0.136 0.028 27 3.1 cuneus
581 411 1575 2.758 0.994 0.103 0.015 4 0.3 entorhinal
4040 2823 6997 2.259 0.578 0.117 0.020 41 3.6 fusiform
6638 4486 13868 2.715 0.729 0.105 0.019 55 5.7 inferiorparietal
3933 2761 6965 2.141 0.765 0.108 0.023 55 3.8 inferiortemporal
1517 1011 2773 2.346 0.995 0.109 0.019 15 1.3 isthmuscingulate
7506 5249 13645 2.330 0.719 0.133 0.032 77 10.2 lateraloccipital
3644 2535 7251 2.615 0.618 0.121 0.022 43 3.7 lateralorbitofrontal
4288 3041 7437 2.160 0.601 0.129 0.027 47 5.5 lingual
2390 1659 4293 2.282 0.782 0.111 0.024 39 2.2 medialorbitofrontal
4220 3000 8931 2.403 0.679 0.108 0.021 44 4.1 middletemporal
976 618 1940 2.609 1.022 0.079 0.011 5 0.4 parahippocampal
2121 1278 3778 2.801 0.606 0.091 0.014 12 1.2 paracentral
2184 1483 4543 2.864 0.673 0.094 0.013 13 1.3 parsopercularis
931 673 2443 2.713 0.592 0.118 0.020 9 0.8 parsorbitalis
1862 1306 3718 2.638 0.538 0.119 0.021 17 1.8 parstriangularis
1878 1289 2405 2.135 0.626 0.117 0.025 16 2.0 pericalcarine
5863 3608 10291 2.459 0.717 0.083 0.011 31 2.9 postcentral
1779 1223 3109 2.391 0.831 0.118 0.017 21 1.5 posteriorcingulate
7251 4423 14389 3.086 0.652 0.088 0.014 39 4.3 precentral
5139 3551 10023 2.749 0.631 0.115 0.020 45 4.5 precuneus
1155 816 2430 2.623 0.745 0.121 0.023 15 1.2 rostralanteriorcingulate
7262 5145 15816 2.683 0.598 0.125 0.028 78 8.6 rostralmiddlefrontal
10939 7290 24221 3.031 0.655 0.112 0.020 89 9.7 superiorfrontal
8443 5348 15694 2.627 0.703 0.099 0.018 63 6.6 superiorparietal
5798 3853 12728 2.962 0.738 0.086 0.012 32 3.4 superiortemporal
4555 3150 10092 2.924 0.676 0.113 0.021 35 4.0 supramarginal
346 277 1288 3.356 0.716 0.158 0.033 5 0.5 frontalpole
558 402 1251 2.573 0.842 0.118 0.020 7 0.5 temporalpole
643 411 1131 2.552 0.388 0.122 0.011 6 0.3 transversetemporal
3488 2412 7266 3.069 0.768 0.115 0.023 32 3.2 insula
mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subjectname lh pial
computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /tmp/tmps594ishs/freesurfer_output/subjectname/mri/wm.mgz...
reading input surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.pial...
reading input pial surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.pial...
reading input white surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 237631
Total vertex volume 237412 (mask=0)
Saving annotation colortable ../label/aparc.annot.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1414190 mm^3 (det: 1.377541 )
1461 785 2159 2.484 0.502 0.066 0.012 8 0.7 bankssts
1060 750 1599 2.141 0.650 0.137 0.043 38 1.4 caudalanteriorcingulate
3468 2606 7254 2.998 0.624 0.105 0.045 47 3.1 caudalmiddlefrontal
2446 2075 4110 2.266 0.667 0.127 0.028 36 2.8 cuneus
581 716 1575 2.758 0.994 0.221 0.042 10 1.3 entorhinal
4040 3506 6997 2.259 0.578 0.138 0.030 82 5.1 fusiform
6638 5542 13868 2.715 0.729 0.112 0.023 94 6.8 inferiorparietal
3933 3834 6965 2.141 0.765 0.157 0.034 53 6.2 inferiortemporal
1517 1310 2773 2.346 0.995 0.144 0.036 29 2.6 isthmuscingulate
7506 6650 13645 2.330 0.719 0.123 0.030 129 9.7 lateraloccipital
3644 3019 7251 2.615 0.618 0.142 0.027 47 4.6 lateralorbitofrontal
4288 3937 7437 2.160 0.601 0.134 0.030 65 6.0 lingual
2390 2254 4293 2.282 0.782 0.157 0.034 35 3.6 medialorbitofrontal
4220 4249 8931 2.403 0.679 0.149 0.030 47 5.9 middletemporal
976 866 1940 2.609 1.022 0.129 0.034 9 1.7 parahippocampal
2121 1415 3778 2.801 0.606 0.085 0.015 16 1.2 paracentral
2184 1718 4543 2.864 0.673 0.112 0.027 42 2.0 parsopercularis
931 1070 2443 2.713 0.592 0.160 0.026 12 1.0 parsorbitalis
1862 1515 3718 2.638 0.538 0.129 0.023 24 1.9 parstriangularis
1878 995 2405 2.135 0.626 0.097 0.028 36 1.9 pericalcarine
5863 4714 10291 2.459 0.717 0.098 0.014 31 3.8 postcentral
1779 1345 3109 2.391 0.831 0.120 0.028 33 1.9 posteriorcingulate
7251 4972 14389 3.086 0.652 0.090 0.015 56 4.6 precentral
5139 3801 10023 2.749 0.631 0.118 0.025 83 5.3 precuneus
1155 1086 2430 2.623 0.745 0.155 0.036 24 1.6 rostralanteriorcingulate
7262 6486 15816 2.683 0.598 0.147 0.031 101 10.0 rostralmiddlefrontal
10939 8521 24221 3.031 0.655 0.113 0.023 131 10.3 superiorfrontal
8443 6599 15694 2.627 0.703 0.113 0.023 136 7.8 superiorparietal
5798 4587 12728 2.962 0.738 0.095 0.017 45 4.3 superiortemporal
4555 3723 10092 2.924 0.676 0.115 0.024 56 4.7 supramarginal
346 484 1288 3.356 0.716 0.187 0.030 3 0.5 frontalpole
558 588 1251 2.573 0.842 0.165 0.027 6 0.7 temporalpole
643 488 1131 2.552 0.388 0.100 0.013 5 0.3 transversetemporal
3488 2243 7266 3.069 0.768 0.130 0.034 89 4.7 insula
#-----------------------------------------
#@# Parcellation Stats rh Fri Jun 13 01:59:42 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab subjectname rh white
computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /tmp/tmps594ishs/freesurfer_output/subjectname/mri/wm.mgz...
reading input surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white...
reading input pial surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.pial...
reading input white surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 234693
Total vertex volume 234487 (mask=0)
Saving annotation colortable ../label/aparc.annot.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1414190 mm^3 (det: 1.377541 )
1230 815 1925 2.483 0.527 0.079 0.010 5 0.5 bankssts
1239 809 1990 2.128 0.662 0.121 0.014 14 0.9 caudalanteriorcingulate
3355 2173 7215 2.995 0.646 0.102 0.019 23 2.6 caudalmiddlefrontal
2309 1591 3898 2.297 0.646 0.130 0.026 24 2.6 cuneus
512 356 1439 2.782 0.947 0.103 0.017 5 0.3 entorhinal
3949 2688 6328 2.196 0.562 0.112 0.020 40 3.4 fusiform
7051 4785 14620 2.668 0.734 0.105 0.019 59 6.0 inferiorparietal
3645 2539 6035 2.072 0.737 0.107 0.024 47 3.6 inferiortemporal
1490 994 2786 2.416 0.988 0.107 0.019 16 1.1 isthmuscingulate
7202 5086 13502 2.350 0.730 0.137 0.033 79 10.1 lateraloccipital
3437 2420 6610 2.561 0.630 0.122 0.023 39 3.7 lateralorbitofrontal
4439 3180 7853 2.142 0.620 0.131 0.027 54 5.7 lingual
2759 1878 4675 2.202 0.745 0.107 0.019 49 2.0 medialorbitofrontal
4618 3128 8789 2.275 0.682 0.102 0.021 47 4.2 middletemporal
1011 628 1979 2.573 1.029 0.083 0.011 7 0.4 parahippocampal
2402 1442 4081 2.760 0.610 0.092 0.015 13 1.6 paracentral
1881 1269 3878 2.884 0.698 0.097 0.015 12 1.2 parsopercularis
1148 834 3067 2.744 0.590 0.124 0.021 12 1.1 parsorbitalis
2216 1549 4293 2.605 0.541 0.113 0.019 19 1.8 parstriangularis
1950 1419 2660 2.148 0.610 0.126 0.026 16 2.4 pericalcarine
5907 3679 10277 2.437 0.705 0.083 0.012 31 3.0 postcentral
1688 1183 2929 2.346 0.807 0.118 0.017 19 1.5 posteriorcingulate
7130 4339 13899 3.062 0.681 0.087 0.013 37 4.0 precentral
5353 3650 10178 2.701 0.612 0.113 0.020 48 4.4 precuneus
886 637 2057 2.791 0.669 0.125 0.021 10 0.9 rostralanteriorcingulate
7563 5337 16378 2.647 0.629 0.125 0.027 81 9.2 rostralmiddlefrontal
10089 6722 22421 3.038 0.655 0.110 0.020 80 8.8 superiorfrontal
8312 5239 15609 2.639 0.696 0.100 0.018 64 6.5 superiorparietal
5673 3745 11809 2.841 0.747 0.086 0.012 33 3.1 superiortemporal
4838 3336 10403 2.828 0.653 0.116 0.021 39 4.5 supramarginal
420 315 1460 3.254 0.664 0.152 0.031 7 0.5 frontalpole
527 369 1196 2.555 0.972 0.117 0.021 7 0.5 temporalpole
547 339 978 2.503 0.353 0.109 0.012 5 0.3 transversetemporal
3476 2422 7270 3.032 0.778 0.116 0.025 32 3.4 insula
mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab subjectname rh pial
computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /tmp/tmps594ishs/freesurfer_output/subjectname/mri/wm.mgz...
reading input surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.pial...
reading input pial surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.pial...
reading input white surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 234693
Total vertex volume 234487 (mask=0)
Saving annotation colortable ../label/aparc.annot.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1414190 mm^3 (det: 1.377541 )
1230 726 1925 2.483 0.527 0.067 0.010 6 0.5 bankssts
1239 944 1990 2.128 0.662 0.138 0.034 39 1.4 caudalanteriorcingulate
3355 2620 7215 2.995 0.646 0.110 0.021 41 3.1 caudalmiddlefrontal
2309 1937 3898 2.297 0.646 0.126 0.028 44 2.3 cuneus
512 685 1439 2.782 0.947 0.264 0.061 12 1.9 entorhinal
3949 3221 6328 2.196 0.562 0.135 0.028 94 4.5 fusiform
7051 5855 14620 2.668 0.734 0.114 0.024 104 7.8 inferiorparietal
3645 3413 6035 2.072 0.737 0.150 0.032 45 5.2 inferiortemporal
1490 1266 2786 2.416 0.988 0.139 0.035 38 2.3 isthmuscingulate
7202 6588 13502 2.350 0.730 0.129 0.030 109 9.6 lateraloccipital
3437 2802 6610 2.561 0.630 0.145 0.030 49 4.7 lateralorbitofrontal
4439 4147 7853 2.142 0.620 0.135 0.029 67 5.9 lingual
2759 2593 4675 2.202 0.745 0.153 0.033 44 4.0 medialorbitofrontal
4618 4461 8789 2.275 0.682 0.145 0.028 47 6.3 middletemporal
1011 880 1979 2.573 1.029 0.132 0.034 10 1.8 parahippocampal
2402 1521 4081 2.760 0.610 0.085 0.015 20 1.4 paracentral
1881 1438 3878 2.884 0.698 0.109 0.023 29 1.7 parsopercularis
1148 1351 3067 2.744 0.590 0.162 0.026 14 1.3 parsorbitalis
2216 1773 4293 2.605 0.541 0.126 0.022 34 2.0 parstriangularis
1950 1160 2660 2.148 0.610 0.108 0.044 89 2.0 pericalcarine
5907 4687 10277 2.437 0.705 0.098 0.014 35 3.7 postcentral
1688 1296 2929 2.346 0.807 0.124 0.029 51 1.6 posteriorcingulate
7130 4809 13899 3.062 0.681 0.089 0.015 55 4.7 precentral
5353 3947 10178 2.701 0.612 0.117 0.025 77 5.7 precuneus
886 856 2057 2.791 0.669 0.152 0.040 19 1.8 rostralanteriorcingulate
7563 6822 16378 2.647 0.629 0.151 0.033 148 11.1 rostralmiddlefrontal
10089 7855 22421 3.038 0.655 0.112 0.022 122 8.8 superiorfrontal
8312 6606 15609 2.639 0.696 0.112 0.021 103 7.6 superiorparietal
5673 4450 11809 2.841 0.747 0.093 0.015 45 3.6 superiortemporal
4838 3901 10403 2.828 0.653 0.115 0.025 61 5.1 supramarginal
420 558 1460 3.254 0.664 0.191 0.031 4 0.6 frontalpole
527 571 1196 2.555 0.972 0.191 0.036 7 1.1 temporalpole
547 455 978 2.503 0.353 0.095 0.011 2 0.2 transversetemporal
3476 2245 7270 3.032 0.778 0.132 0.039 76 5.6 insula
#-----------------------------------------
#@# Parcellation Stats 2 lh Fri Jun 13 01:59:58 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab subjectname lh white
computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /tmp/tmps594ishs/freesurfer_output/subjectname/mri/wm.mgz...
reading input surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white...
reading input pial surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.pial...
reading input white surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 237631
Total vertex volume 237412 (mask=0)
Saving annotation colortable ../label/aparc.annot.a2009s.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1414190 mm^3 (det: 1.377541 )
1095 814 2474 2.675 0.610 0.145 0.037 16 1.8 G_and_S_frontomargin
1487 1056 3176 2.468 0.765 0.140 0.033 17 1.9 G_and_S_occipital_inf
1658 926 2920 2.736 0.664 0.095 0.015 12 1.1 G_and_S_paracentral
1209 882 2741 2.607 0.649 0.129 0.021 12 1.1 G_and_S_subcentral
579 443 2014 3.326 0.663 0.154 0.033 9 0.9 G_and_S_transv_frontopol
2082 1506 3854 2.463 0.707 0.110 0.019 18 1.8 G_and_S_cingul-Ant
1353 927 2361 2.560 0.478 0.107 0.013 9 1.1 G_and_S_cingul-Mid-Ant
1294 915 2453 2.714 0.469 0.109 0.018 10 1.1 G_and_S_cingul-Mid-Post
621 420 1789 3.278 0.648 0.139 0.022 9 0.6 G_cingul-Post-dorsal
266 167 658 2.859 0.923 0.101 0.018 3 0.2 G_cingul-Post-ventral
2267 1528 4023 2.242 0.709 0.133 0.029 26 2.7 G_cuneus
1200 871 3411 2.994 0.521 0.123 0.017 13 1.0 G_front_inf-Opercular
353 251 1051 2.964 0.460 0.128 0.025 4 0.5 G_front_inf-Orbital
1055 775 2698 2.713 0.567 0.140 0.027 14 1.3 G_front_inf-Triangul
4475 3039 12165 2.981 0.643 0.129 0.029 55 5.5 G_front_middle
7539 4882 19044 3.215 0.586 0.120 0.022 77 7.2 G_front_sup
708 475 1538 3.226 0.739 0.114 0.022 8 0.5 G_Ins_lg_and_S_cent_ins
655 511 2447 3.645 0.784 0.145 0.027 9 1.0 G_insular_short
2423 1700 5996 2.705 0.748 0.132 0.031 33 3.2 G_occipital_middle
1591 1067 3125 2.467 0.826 0.128 0.033 14 2.3 G_occipital_sup
1760 1222 3731 2.547 0.561 0.127 0.026 22 2.1 G_oc-temp_lat-fusifor
3000 2158 6024 2.221 0.666 0.142 0.033 39 4.7 G_oc-temp_med-Lingual
1252 824 3234 2.858 0.940 0.100 0.016 11 0.7 G_oc-temp_med-Parahip
2124 1557 5841 2.752 0.620 0.130 0.024 32 2.2 G_orbital
2321 1529 6333 3.023 0.834 0.113 0.023 24 2.3 G_pariet_inf-Angular
2117 1505 5660 3.075 0.660 0.127 0.024 20 2.1 G_pariet_inf-Supramar
3358 1979 7518 2.836 0.752 0.095 0.018 29 2.6 G_parietal_sup
2192 1213 4601 2.799 0.651 0.085 0.012 13 1.2 G_postcentral
2801 1438 6685 3.433 0.541 0.081 0.014 16 1.6 G_precentral
2405 1610 5916 2.822 0.666 0.124 0.023 29 2.3 G_precuneus
872 593 1840 2.397 0.720 0.108 0.022 20 0.9 G_rectus
569 393 1081 2.775 0.871 0.141 0.054 13 1.0 G_subcallosal
489 292 997 2.713 0.432 0.100 0.009 4 0.2 G_temp_sup-G_T_transv
1895 1311 5867 3.351 0.709 0.108 0.017 18 1.6 G_temp_sup-Lateral
676 453 1431 2.828 0.761 0.062 0.010 2 0.3 G_temp_sup-Plan_polar
1086 737 2358 2.759 0.528 0.108 0.021 7 1.0 G_temp_sup-Plan_tempo
2173 1617 5089 2.294 0.843 0.121 0.028 42 2.8 G_temporal_inf
2215 1661 6032 2.615 0.705 0.133 0.029 37 2.9 G_temporal_middle
310 201 359 2.282 0.390 0.084 0.011 1 0.1 Lat_Fis-ant-Horizont
406 275 583 2.653 0.506 0.096 0.015 2 0.3 Lat_Fis-ant-Vertical
1048 687 1365 2.721 0.340 0.099 0.014 6 0.7 Lat_Fi
s-post
1982 1412 3892 2.259 0.813 0.143 0.036 25 3.1 Pole_occipital
1166 854 2418 2.353 0.590 0.126 0.029 18 1.3 Pole_temporal
2414 1680 3118 2.161 0.628 0.110 0.022 18 2.4 S_calcarine
3154 2128 4338 2.383 0.818 0.077 0.009 11 1.3 S_central
1076 712 1566 2.509 0.606 0.084 0.010 4 0.5 S_cingul-Marginalis
503 335 838 3.089 0.482 0.092 0.016 2 0.3 S_circular_insula_ant
1476 983 2373 2.913 0.719 0.069 0.010 4 0.6 S_circular_insula_inf
1774 1151 2327 2.656 0.420 0.092 0.013 7 1.1 S_circular_insula_sup
821 551 862 1.764 0.434 0.090 0.009 4 0.3 S_collat_transv_ant
481 338 527 2.057 0.320 0.151 0.040 4 0.8 S_collat_transv_post
1863 1238 2674 2.394 0.488 0.086 0.013 9 0.8 S_front_inf
1470 1006 1916 2.524 0.537 0.111 0.020 9 1.6 S_front_middle
2673 1826 4695 2.838 0.574 0.092 0.016 14 1.6 S_front_sup
278 189 377 2.530 0.741 0.122 0.027 2 0.4 S_interm_prim-Jensen
3276 2224 4431 2.388 0.595 0.097 0.015 20 2.3 S_intrapariet_and_P_trans
1079 728 1365 2.302 0.372 0.101 0.018 5 0.8 S_oc_middle_and_Lunatus
1200 837 1893 2.598 0.581 0.100 0.015 6 0.8 S_oc_sup_and_transversal
661 434 769 2.092 0.477 0.107 0.017 4 0.6 S_occipital_ant
746 489 970 2.294 0.679 0.084 0.013 3 0.4 S_oc-temp_lat
2012 1377 2468 2.062 0.543 0.091 0.011 10 0.9 S_oc-temp_med_and_Lingual
446 304 612 2.254 0.480 0.092 0.015 2 0.4 S_orbital_lateral
702 476 769 1.827 0.655 0.108 0.016 5 0.5 S_orbital_med-olfact
1369 949 2301 2.513 0.458 0.119 0.023 13 1.5 S_orbital-H_Shaped
2033 1445 3322 2.737 0.581 0.113 0.019 15 1.8 S_parieto_occipital
1555 966 1178 1.498 0.582 0.113 0.015 21 1.1 S_pericallosal
2343 1536 3392 2.496 0.643 0.076 0.013 9 1.1 S_postcentral
1523 996 2422 2.877 0.604 0.084 0.011 6 0.8 S_precentral-inf-part
1440 980 2406 2.971 0.547 0.093 0.017 6 1.1 S_precentral-sup-part
753 520 1165 2.187 0.661 0.121 0.019 7 0.6 S_suborbital
1040 732 1580 2.703 0.462 0.110 0.017 6 0.8 S_subparietal
1304 874 1428 1.816 0.497 0.102 0.018 8 0.9 S_temporal_inf
6448 4215 10145 2.551 0.649 0.082 0.011 27 3.3 S_temporal_sup
323 225 398 2.051 0.405 0.118 0.009 2 0.2 S_temporal_transverse
#-----------------------------------------
#@# Parcellation Stats 2 rh Fri Jun 13 02:00:06 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab subjectname rh white
computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /tmp/tmps594ishs/freesurfer_output/subjectname/mri/wm.mgz...
reading input surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white...
reading input pial surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.pial...
reading input white surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 234693
Total vertex volume 234487 (mask=0)
Saving annotation colortable ../label/aparc.annot.a2009s.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1414190 mm^3 (det: 1.377541 )
854 636 1944 2.581 0.618 0.140 0.033 13 1.2 G_and_S_frontomargin
1228 857 2558 2.458 0.778 0.142 0.026 15 1.3 G_and_S_occipital_inf
1534 848 2595 2.680 0.613 0.096 0.015 11 1.0 G_and_S_paracentral
1249 884 2550 2.514 0.580 0.125 0.020 12 1.0 G_and_S_subcentral
1060 790 3241 3.096 0.744 0.156 0.036 17 1.6 G_and_S_transv_frontopol
2837 2001 5009 2.385 0.714 0.111 0.019 27 2.2 G_and_S_cingul-Ant
1538 1053 2759 2.576 0.531 0.110 0.014 11 1.2 G_and_S_cingul-Mid-Ant
1379 964 2585 2.709 0.482 0.111 0.018 11 1.2 G_and_S_cingul-Mid-Post
543 356 1543 3.230 0.602 0.133 0.023 7 0.6 G_cingul-Post-dorsal
289 180 785 3.122 0.803 0.107 0.024 3 0.2 G_cingul-Post-ventral
2277 1523 3888 2.254 0.657 0.130 0.026 27 2.5 G_cuneus
1147 817 3186 2.938 0.508 0.122 0.018 12 1.0 G_front_inf-Opercular
458 333 1335 2.916 0.449 0.154 0.033 7 0.6 G_front_inf-Orbital
912 677 2171 2.649 0.564 0.138 0.024 12 1.1 G_front_inf-Triangul
4048 2782 11666 2.984 0.671 0.134 0.029 51 5.3 G_front_middle
6585 4239 17046 3.271 0.577 0.118 0.023 63 6.4 G_front_sup
594 421 1491 3.290 0.862 0.099 0.021 6 0.3 G_Ins_lg_and_S_cent_ins
659 505 2306 3.566 0.821 0.144 0.028 9 0.9 G_insular_short
2383 1718 6313 2.832 0.798 0.129 0.029 32 2.8 G_occipital_middle
1516 936 3386 2.722 0.763 0.118 0.031 13 2.0 G_occipital_sup
1908 1260 3822 2.476 0.572 0.126 0.027 27 2.3 G_oc-temp_lat-fusifor
2700 1888 5364 2.241 0.659 0.133 0.029 36 3.8 G_oc-temp_med-Lingual
1027 645 2851 2.983 0.941 0.094 0.016 9 0.5 G_oc-temp_med-Parahip
2397 1765 6596 2.770 0.650 0.129 0.030 36 2.7 G_orbital
2368 1613 6922 3.034 0.794 0.123 0.026 28 2.7 G_pariet_inf-Angular
2391 1711 6154 2.937 0.650 0.130 0.024 24 2.4 G_pariet_inf-Supramar
3185 1900 6770 2.704 0.810 0.097 0.019 31 2.5 G_parietal_sup
2114 1212 4483 2.742 0.649 0.088 0.012 14 1.2 G_postcentral
2675 1345 6368 3.443 0.603 0.078 0.013 15 1.4 G_precentral
2345 1512 5448 2.770 0.652 0.118 0.023 27 2.2 G_precuneus
779 510 1583 2.384 0.720 0.114 0.024 30 0.8 G_rectus
444 288 789 2.597 0.862 0.093 0.026 4 0.4 G_subcallosal
434 254 867 2.639 0.364 0.102 0.010 4 0.2 G_temp_sup-G_T_transv
1918 1302 5757 3.372 0.607 0.108 0.018 18 1.6 G_temp_sup-Lateral
845 542 1551 2.666 0.804 0.070 0.018 4 0.6 G_temp_sup-Plan_polar
950 653 1936 2.664 0.466 0.099 0.018 5 0.8 G_temp_sup-Plan_tempo
1659 1227 3636 2.198 0.813 0.124 0.032 34 2.4 G_temporal_inf
2904 2000 6877 2.490 0.696 0.120 0.028 42 3.5 G_temporal_middle
346 227 400 2.260 0.364 0.079 0.008 1 0.1 Lat_Fis-ant-Horizont
423 282 587 2.533 0.488 0.096 0.019 2 0.3 Lat_Fis-ant-Vertical
1373 897 1759 2.571 0.310 0.100 0.015 7 0.9 Lat_Fi
s-post
3288 2371 6331 2.180 0.780 0.149 0.037 42 5.4 Pole_occipital
1257 914 2444 2.198 0.596 0.126 0.028 19 1.4 Pole_temporal
2272 1658 3101 2.205 0.623 0.118 0.023 17 2.7 S_calcarine
3072 2076 4219 2.400 0.826 0.076 0.009 10 1.3 S_central
1240 826 1857 2.495 0.621 0.084 0.010 5 0.5 S_cingul-Marginalis
546 368 898 2.986 0.566 0.092 0.015 2 0.4 S_circular_insula_ant
1244 810 1764 2.735 0.732 0.068 0.007 3 0.4 S_circular_insula_inf
1555 993 2144 2.737 0.462 0.090 0.012 6 0.9 S_circular_insula_sup
871 598 969 1.807 0.508 0.085 0.008 4 0.3 S_collat_transv_ant
393 286 459 1.960 0.306 0.151 0.037 3 0.7 S_collat_transv_post
1928 1242 2548 2.282 0.404 0.080 0.013 9 0.7 S_front_inf
2029 1390 2902 2.533 0.523 0.106 0.021 12 2.0 S_front_middle
2533 1706 4213 2.813 0.551 0.091 0.015 12 1.5 S_front_sup
330 228 519 2.712 0.770 0.104 0.021 2 0.3 S_interm_prim-Jensen
3209 2168 4610 2.434 0.552 0.095 0.015 19 2.0 S_intrapariet_and_P_trans
941 662 1210 2.197 0.407 0.111 0.023 6 1.0 S_oc_middle_and_Lunatus
1241 867 1882 2.531 0.579 0.106 0.017 7 1.0 S_oc_sup_and_transversal
631 424 802 2.215 0.687 0.101 0.017 4 0.5 S_occipital_ant
874 583 1131 2.210 0.677 0.084 0.014 3 0.4 S_oc-temp_lat
2138 1475 2634 2.064 0.545 0.093 0.012 11 1.0 S_oc-temp_med_and_Lingual
319 219 430 2.244 0.444 0.091 0.013 1 0.2 S_orbital_lateral
746 552 920 1.892 0.708 0.125 0.021 6 0.7 S_orbital_med-olfact
1333 947 2309 2.502 0.444 0.124 0.023 12 1.4 S_orbital-H_Shaped
2012 1434 3260 2.721 0.534 0.113 0.019 15 1.8 S_parieto_occipital
1632 1058 1478 1.588 0.647 0.115 0.016 23 1.1 S_pericallosal
2163 1399 3060 2.508 0.687 0.075 0.012 8 1.0 S_postcentral
1547 1012 2428 2.899 0.698 0.086 0.012 7 0.8 S_precentral-inf-part
1437 982 2281 2.886 0.556 0.093 0.016 6 1.0 S_precentral-sup-part
342 228 494 2.160 0.638 0.108 0.015 2 0.2 S_suborbital
1315 930 2222 2.698 0.522 0.113 0.018 9 1.0 S_subparietal
1130 762 1179 1.714 0.420 0.098 0.017 7 0.8 S_temporal_inf
6110 3962 8570 2.405 0.606 0.078 0.010 22 2.8 S_temporal_sup
299 210 345 1.921 0.349 0.125 0.011 2 0.2 S_temporal_transverse
#-----------------------------------------
#@# Parcellation Stats 3 lh Fri Jun 13 02:00:14 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab subjectname lh white
computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /tmp/tmps594ishs/freesurfer_output/subjectname/mri/wm.mgz...
reading input surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white...
reading input pial surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.pial...
reading input white surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 237631
Total vertex volume 237412 (mask=0)
Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1414190 mm^3 (det: 1.377541 )
1974 1289 3544 2.412 0.714 0.114 0.013 20 1.2 caudalanteriorcingulate
3731 2422 7849 2.980 0.617 0.104 0.020 27 3.1 caudalmiddlefrontal
3235 2217 5375 2.327 0.673 0.129 0.025 33 3.7 cuneus
525 370 1489 2.817 0.999 0.101 0.015 4 0.3 entorhinal
3761 2615 6465 2.274 0.583 0.114 0.020 36 3.3 fusiform
6610 4469 14212 2.746 0.739 0.106 0.019 56 5.7 inferiorparietal
3850 2728 6652 2.101 0.741 0.113 0.023 56 3.7 inferiortemporal
1519 1014 2808 2.386 0.998 0.109 0.019 15 1.3 isthmuscingulate
7555 5244 13921 2.356 0.726 0.133 0.032 78 10.5 lateraloccipital
3862 2744 8201 2.605 0.642 0.130 0.026 53 4.6 lateralorbitofrontal
4456 3167 7674 2.150 0.599 0.130 0.027 49 5.8 lingual
2164 1518 4112 2.346 0.805 0.113 0.025 33 1.9 medialorbitofrontal
5703 3989 11373 2.384 0.642 0.102 0.019 53 5.0 middletemporal
1037 658 2057 2.617 1.014 0.080 0.011 6 0.4 parahippocampal
2516 1565 4472 2.797 0.600 0.096 0.015 15 1.7 paracentral
2017 1367 4181 2.892 0.673 0.099 0.014 13 1.2 parsopercularis
974 680 2352 2.927 0.504 0.110 0.018 7 0.9 parsorbitalis
2213 1536 4353 2.608 0.547 0.110 0.019 18 1.9 parstriangularis
1830 1259 2339 2.140 0.635 0.117 0.025 15 1.9 pericalcarine
6532 4053 11294 2.439 0.702 0.085 0.012 36 3.4 postcentral
1941 1320 3299 2.403 0.804 0.117 0.017 22 1.6 posteriorcingulate
7185 4377 14132 3.083 0.659 0.088 0.013 39 4.0 precentral
5054 3499 10202 2.754 0.650 0.117 0.021 47 4.6 precuneus
1566 1100 2937 2.499 0.754 0.126 0.027 23 1.9 rostralanteriorcingulate
5308 3735 11286 2.670 0.583 0.123 0.027 54 6.0 rostralmiddlefrontal
11395 7697 26139 3.027 0.674 0.115 0.022 102 11.1 superiorfrontal
6791 4281 12727 2.675 0.688 0.096 0.016 48 4.8 superiorparietal
7348 4918 15510 2.884 0.741 0.089 0.013 44 4.4 superiortemporal
4247 2922 9049 2.922 0.660 0.113 0.021 32 3.8 supramarginal
649 413 1137 2.564 0.419 0.121 0.011 6 0.3 transversetemporal
2815 1952 6273 3.153 0.762 0.103 0.017 21 2.1 insula
#-----------------------------------------
#@# Parcellation Stats 3 rh Fri Jun 13 02:00:22 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname/scripts
mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab subjectname rh white
computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /tmp/tmps594ishs/freesurfer_output/subjectname/mri/wm.mgz...
reading input surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white...
reading input pial surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.pial...
reading input white surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 234693
Total vertex volume 234487 (mask=0)
Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1414190 mm^3 (det: 1.377541 )
1368 899 2320 2.184 0.703 0.123 0.014 16 1.0 caudalanteriorcingulate
3486 2265 7384 2.968 0.655 0.103 0.020 25 2.9 caudalmiddlefrontal
2816 1923 4783 2.369 0.666 0.129 0.025 30 3.1 cuneus
488 339 1420 2.823 0.982 0.105 0.017 5 0.3 entorhinal
3634 2461 5866 2.223 0.565 0.109 0.020 34 3.0 fusiform
7018 4752 14702 2.694 0.735 0.106 0.019 59 6.1 inferiorparietal
3999 2807 6568 2.054 0.713 0.111 0.024 53 3.9 inferiortemporal
1457 975 2737 2.425 0.968 0.108 0.019 16 1.1 isthmuscingulate
7306 5133 13876 2.362 0.736 0.136 0.033 79 10.1 lateraloccipital
4007 2896 8409 2.585 0.650 0.136 0.031 56 5.3 lateralorbitofrontal
4375 3138 7752 2.135 0.615 0.130 0.027 51 5.6 lingual
2077 1410 3947 2.342 0.810 0.112 0.022 42 1.9 medialorbitofrontal
5563 3755 10230 2.271 0.648 0.098 0.020 52 4.7 middletemporal
1039 647 2022 2.584 1.024 0.082 0.012 7 0.4 parahippocampal
2519 1525 4275 2.759 0.606 0.092 0.014 14 1.6 paracentral
2117 1416 4143 2.802 0.708 0.095 0.014 13 1.3 parsopercularis
963 675 2355 2.829 0.554 0.107 0.018 8 0.7 parsorbitalis
2203 1543 4335 2.606 0.558 0.115 0.020 19 2.0 parstriangularis
1912 1389 2644 2.180 0.609 0.124 0.025 15 2.3 pericalcarine
6461 4035 11184 2.432 0.697 0.085 0.012 36 3.4 postcentral
1757 1220 2994 2.346 0.809 0.118 0.018 20 1.5 posteriorcingulate
6922 4211 13591 3.067 0.684 0.087 0.013 36 3.9 precentral
5553 3779 10751 2.698 0.640 0.114 0.021 53 4.9 precuneus
1155 806 2344 2.590 0.768 0.115 0.020 12 1.0 rostralanteriorcingulate
5455 3838 11529 2.633 0.606 0.123 0.027 54 6.5 rostralmiddlefrontal
12570 8498 28012 2.960 0.694 0.114 0.021 112 11.6 superiorfrontal
6837 4297 12779 2.660 0.688 0.098 0.017 51 5.1 superiorparietal
7013 4657 14342 2.801 0.752 0.089 0.013 45 4.0 superiortemporal
4668 3220 9803 2.808 0.650 0.114 0.021 37 4.3 supramarginal
551 343 999 2.553 0.378 0.115 0.012 5 0.3 transversetemporal
2963 2039 6388 3.072 0.776 0.102 0.016 22 1.9 insula
#--------------------------------------------
#@# ASeg Stats Fri Jun 13 02:00:30 UTC 2025
/tmp/tmps594ishs/freesurfer_output/subjectname
mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer-7.3.2/ASegStatsLUT.txt --subject subjectname
setting seed for random number genererator to 1234
7.3.2
cwd
cmdline mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer-7.3.2/ASegStatsLUT.txt --subject subjectname
sysname Linux
hostname fv-az1121-699
machine x86_64
user runner
whitesurfname white
UseRobust 0
atlas_icv (eTIV) = 1414190 mm^3 (det: 1.377541 )
Computing euler number
orig.nofix lheno = -20, rheno = -24
orig.nofix lhholes = 11, rhholes = 13
Loading mri/aseg.mgz
Getting Brain Volume Statistics
Loading mri/norm.mgz
Loading mri/norm.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 50 segmentations
Computing statistics for each segmentation
Reporting on 45 segmentations
Using PrintSegStat
mri_segstats done
/tmp/tmps594ishs/freesurfer_output/subjectname/label
INFO: fsaverage subject does not exist in SUBJECTS_DIR
INFO: Creating symlink to fsaverage subject...
cd /tmp/tmps594ishs/freesurfer_output; ln -s /opt/freesurfer-7.3.2/subjects/fsaverage; cd -
#--------------------------------------------
#@# BA_exvivo Labels lh Fri Jun 13 02:02:13 UTC 2025
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA1_exvivo.label --trgsubject subjectname --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA1_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.BA1_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 4129 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 4129 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 63
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4192
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA2_exvivo.label --trgsubject subjectname --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA2_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.BA2_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 7909 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 7909 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 63
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 7972
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA3a_exvivo.label --trgsubject subjectname --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA3a_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.BA3a_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 4077 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 4077 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 28
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4105
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA3b_exvivo.label --trgsubject subjectname --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA3b_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.BA3b_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 5983 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 5983 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 70
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6053
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA4a_exvivo.label --trgsubject subjectname --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA4a_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.BA4a_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 5784 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 5784 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 165
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 5949
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA4p_exvivo.label --trgsubject subjectname --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA4p_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.BA4p_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 4070 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 4070 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 96
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4166
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA6_exvivo.label --trgsubject subjectname --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA6_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.BA6_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 13589 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 13589 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 882
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 14471
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA44_exvivo.label --trgsubject subjectname --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA44_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.BA44_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 4181 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 4181 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 54
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4235
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA45_exvivo.label --trgsubject subjectname --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA45_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.BA45_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 3422 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 3422 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 258
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 3680
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.V1_exvivo.label --trgsubject subjectname --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.V1_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.V1_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 4641 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 4641 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 927
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 5568
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.V2_exvivo.label --trgsubject subjectname --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.V2_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.V2_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 8114 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 8114 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 2478
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 10592
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.MT_exvivo.label --trgsubject subjectname --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.MT_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.MT_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 2018 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 2018 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 304
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2322
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject subjectname --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.entorhinal_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.entorhinal_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 1290 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 1290 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 28
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1318
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject subjectname --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.perirhinal_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.perirhinal_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 1199 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 1199 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 20
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1219
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject subjectname --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.FG1.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.FG1.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 414 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 414 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 56
Checking for and removing duplicates
Writing label file ./lh.FG1.mpm.vpnl.label 470
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject subjectname --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.FG2.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.FG2.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 703 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 703 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 112
Checking for and removing duplicates
Writing label file ./lh.FG2.mpm.vpnl.label 815
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject subjectname --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.FG3.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.FG3.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 1873 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 1873 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 91
Checking for and removing duplicates
Writing label file ./lh.FG3.mpm.vpnl.label 1964
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject subjectname --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.FG4.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.FG4.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 2101 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 2101 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 196
Checking for and removing duplicates
Writing label file ./lh.FG4.mpm.vpnl.label 2297
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject subjectname --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.hOc1.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.hOc1.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 3877 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 3877 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 702
Checking for and removing duplicates
Writing label file ./lh.hOc1.mpm.vpnl.label 4579
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject subjectname --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.hOc2.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.hOc2.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 2919 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 2919 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 1228
Checking for and removing duplicates
Writing label file ./lh.hOc2.mpm.vpnl.label 4147
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject subjectname --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.hOc3v.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.hOc3v.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 1286 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 1286 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 497
Checking for and removing duplicates
Writing label file ./lh.hOc3v.mpm.vpnl.label 1783
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject subjectname --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.hOc4v.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.hOc4v.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 1006 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 1006 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 316
Checking for and removing duplicates
Writing label file ./lh.hOc4v.mpm.vpnl.label 1322
mri_label2label: Done
mris_label2annot --s subjectname --ctab /opt/freesurfer-7.3.2/average/colortable_vpnl.txt --hemi lh --a mpm.vpnl --maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l lh.FG2.mpm.vpnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label --l lh.hOc1.mpm.vpnl.label --l lh.hOc2.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl.label --l lh.hOc4v.mpm.vpnl.label
Reading ctab /opt/freesurfer-7.3.2/average/colortable_vpnl.txt
Number of ctab entries 9
7.3.2
cwd /tmp/tmps594ishs/freesurfer_output/subjectname/label
cmdline mris_label2annot --s subjectname --ctab /opt/freesurfer-7.3.2/average/colortable_vpnl.txt --hemi lh --a mpm.vpnl --maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l lh.FG2.mpm.vpnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label --l lh.hOc1.mpm.vpnl.label --l lh.hOc2.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl.label --l lh.hOc4v.mpm.vpnl.label
sysname Linux
hostname fv-az1121-699
machine x86_64
user runner
subject subjectname
hemi lh
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
ColorTable /opt/freesurfer-7.3.2/average/colortable_vpnl.txt
AnnotName mpm.vpnl
nlables 8
LabelThresh 0 0.000000
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.orig
1 1376057 FG1
2 16711935 FG2
3 16711680 FG3
4 1705837 FG4
5 25600 hOc1
6 255 hOc2
7 16776960 hOc3v
8 65535 hOc4v
Mapping unhit to unknown
Found 113190 unhit vertices
Writing annot to /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.mpm.vpnl.annot
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject subjectname --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA1_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.BA1_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 1014 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 1014 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 14
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1028
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject subjectname --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA2_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.BA2_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 2092 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 2092 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 18
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2110
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject subjectname --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA3a_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.BA3a_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 1504 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 1504 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 9
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1513
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject subjectname --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA3b_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.BA3b_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 1996 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 1996 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 39
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2035
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject subjectname --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA4a_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.BA4a_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 2319 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 2319 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 57
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2376
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject subjectname --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA4p_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.BA4p_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 1549 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 1549 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 23
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1572
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject subjectname --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA6_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.BA6_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 7035 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 7035 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 347
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 7382
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject subjectname --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA44_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.BA44_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 1912 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 1912 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 19
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 1931
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject subjectname --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.BA45_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.BA45_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 1151 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 1151 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 162
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1313
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject subjectname --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.V1_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.V1_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 3405 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 3405 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 561
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 3966
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject subjectname --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.V2_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.V2_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 3334 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 3334 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 1275
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 4609
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject subjectname --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.MT_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.MT_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 513 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 513 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 67
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 580
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject subjectname --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.entorhinal_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.entorhinal_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 470 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 470 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 13
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 483
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject subjectname --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/lh.perirhinal_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./lh.perirhinal_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 450 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/lh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 450 nlabel points
Performing mapping from target back to the source label 128612
Number of reverse mapping hits = 11
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 461
mri_label2label: Done
mris_label2annot --s subjectname --hemi lh --ctab /opt/freesurfer-7.3.2/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.perirhinal_exvivo.label --l lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose
Reading ctab /opt/freesurfer-7.3.2/average/colortable_BA.txt
Number of ctab entries 15
7.3.2
cwd /tmp/tmps594ishs/freesurfer_output/subjectname/label
cmdline mris_label2annot --s subjectname --hemi lh --ctab /opt/freesurfer-7.3.2/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.perirhinal_exvivo.label --l lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose
sysname Linux
hostname fv-az1121-699
machine x86_64
user runner
subject subjectname
hemi lh
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
ColorTable /opt/freesurfer-7.3.2/average/colortable_BA.txt
AnnotName BA_exvivo
nlables 14
LabelThresh 0 0.000000
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.orig
1 1530880 BA1_exvivo
2 16749699 BA2_exvivo
3 16711680 BA3a_exvivo
4 3368703 BA3b_exvivo
5 1376196 BA4a_exvivo
6 13382655 BA4p_exvivo
7 10036737 BA6_exvivo
8 2490521 BA44_exvivo
9 39283 BA45_exvivo
10 3993 V1_exvivo
11 8508928 V2_exvivo
12 10027163 MT_exvivo
13 16422433 perirhinal_exvivo
14 16392598 entorhinal_exvivo
Mapping unhit to unknown
Found 88680 unhit vertices
Writing annot to /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.BA_exvivo.annot
mris_label2annot --s subjectname --hemi lh --ctab /opt/freesurfer-7.3.2/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose
Reading ctab /opt/freesurfer-7.3.2/average/colortable_BA.txt
Number of ctab entries 15
7.3.2
cwd /tmp/tmps594ishs/freesurfer_output/subjectname/label
cmdline mris_label2annot --s subjectname --hemi lh --ctab /opt/freesurfer-7.3.2/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose
sysname Linux
hostname fv-az1121-699
machine x86_64
user runner
subject subjectname
hemi lh
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
ColorTable /opt/freesurfer-7.3.2/average/colortable_BA.txt
AnnotName BA_exvivo.thresh
nlables 14
LabelThresh 0 0.000000
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.orig
1 1530880 BA1_exvivo
2 16749699 BA2_exvivo
3 16711680 BA3a_exvivo
4 3368703 BA3b_exvivo
5 1376196 BA4a_exvivo
6 13382655 BA4p_exvivo
7 10036737 BA6_exvivo
8 2490521 BA44_exvivo
9 39283 BA45_exvivo
10 3993 V1_exvivo
11 8508928 V2_exvivo
12 10027163 MT_exvivo
13 16422433 perirhinal_exvivo
14 16392598 entorhinal_exvivo
Mapping unhit to unknown
Found 104722 unhit vertices
Writing annot to /tmp/tmps594ishs/freesurfer_output/subjectname/label/lh.BA_exvivo.thresh.annot
mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab subjectname lh white
computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /tmp/tmps594ishs/freesurfer_output/subjectname/mri/wm.mgz...
reading input surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white...
reading input pial surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.pial...
reading input white surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 237631
Total vertex volume 237412 (mask=0)
Saving annotation colortable ./BA_exvivo.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1414190 mm^3 (det: 1.377541 )
1090 593 2400 2.773 0.541 0.098 0.015 9 0.6 BA1_exvivo
3172 2017 5712 2.690 0.667 0.078 0.012 13 1.5 BA2_exvivo
1024 717 1131 2.100 0.416 0.110 0.015 6 0.6 BA3a_exvivo
2235 1434 3323 2.071 0.622 0.085 0.012 12 1.3 BA3b_exvivo
1696 887 3437 3.383 0.473 0.072 0.011 8 0.7 BA4a_exvivo
1304 805 2532 3.331 0.587 0.070 0.009 4 0.5 BA4p_exvivo
9959 6165 22297 3.189 0.582 0.101 0.018 69 7.6 BA6_exvivo
2012 1401 4377 2.877 0.672 0.100 0.013 15 1.3 BA44_exvivo
2640 1852 5495 2.618 0.508 0.111 0.020 22 2.1 BA45_exvivo
3321 2341 5074 2.090 0.642 0.120 0.026 32 3.8 V1_exvivo
8376 5919 14694 2.206 0.661 0.141 0.034 93 12.6 V2_exvivo
1983 1338 3314 2.333 0.724 0.116 0.023 19 1.9 MT_exvivo
583 428 937 2.066 0.610 0.111 0.017 5 0.4 perirhinal_exvivo
537 358 1756 3.287 0.945 0.090 0.017 5 0.4 entorhinal_exvivo
mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab subjectname lh white
computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /tmp/tmps594ishs/freesurfer_output/subjectname/mri/wm.mgz...
reading input surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white...
reading input pial surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.pial...
reading input white surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 237631
Total vertex volume 237412 (mask=0)
Saving annotation colortable ./BA_exvivo.thresh.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1414190 mm^3 (det: 1.377541 )
717 373 1631 2.842 0.525 0.111 0.016 7 0.5 BA1_exvivo
1350 816 2759 2.990 0.630 0.056 0.008 3 0.4 BA2_exvivo
900 630 971 2.115 0.432 0.113 0.016 5 0.6 BA3a_exvivo
1430 903 1677 1.790 0.410 0.066 0.006 5 0.5 BA3b_exvivo
1605 896 3328 3.438 0.473 0.068 0.011 6 0.7 BA4a_exvivo
1077 658 1961 3.224 0.583 0.073 0.009 4 0.4 BA4p_exvivo
5469 3250 11993 3.222 0.584 0.094 0.015 33 3.7 BA6_exvivo
1285 898 2936 2.983 0.713 0.105 0.014 10 0.9 BA44_exvivo
1165 834 2627 2.660 0.528 0.125 0.022 12 1.2 BA45_exvivo
3510 2485 5567 2.114 0.632 0.121 0.026 35 4.0 V1_exvivo
4282 3038 7424 2.136 0.733 0.145 0.036 50 6.9 V2_exvivo
502 342 968 2.594 0.816 0.109 0.020 5 0.4 MT_exvivo
260 188 346 2.008 0.412 0.106 0.015 1 0.2 perirhinal_exvivo
338 227 1012 3.236 0.805 0.070 0.007 1 0.1 entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Fri Jun 13 02:04:19 UTC 2025
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA1_exvivo.label --trgsubject subjectname --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA1_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.BA1_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 3962 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 3962 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 110
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4072
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA2_exvivo.label --trgsubject subjectname --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA2_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.BA2_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 6687 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 6687 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 115
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 6802
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA3a_exvivo.label --trgsubject subjectname --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA3a_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.BA3a_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 3980 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 3980 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 37
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4017
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA3b_exvivo.label --trgsubject subjectname --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA3b_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.BA3b_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 4522 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 4522 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 101
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 4623
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA4a_exvivo.label --trgsubject subjectname --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA4a_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.BA4a_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 5747 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 5747 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 176
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 5923
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA4p_exvivo.label --trgsubject subjectname --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA4p_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.BA4p_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 4473 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 4473 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 99
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 4572
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA6_exvivo.label --trgsubject subjectname --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA6_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.BA6_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 12256 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 12256 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 605
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 12861
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA44_exvivo.label --trgsubject subjectname --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA44_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.BA44_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 6912 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 6912 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 257
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 7169
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA45_exvivo.label --trgsubject subjectname --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA45_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.BA45_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 5355 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 5355 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 436
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 5791
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.V1_exvivo.label --trgsubject subjectname --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.V1_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.V1_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 4727 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 4727 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 949
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 5676
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.V2_exvivo.label --trgsubject subjectname --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.V2_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.V2_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 8016 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 8016 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 2134
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 10150
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.MT_exvivo.label --trgsubject subjectname --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.MT_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.MT_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 1932 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 1932 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 254
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2186
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject subjectname --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.entorhinal_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.entorhinal_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 1038 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 1038 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 17
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1055
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject subjectname --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.perirhinal_exvivo.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.perirhinal_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 752 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 752 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 8
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 760
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.FG1.mpm.vpnl.label --trgsubject subjectname --trglabel ./rh.FG1.mpm.vpnl.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.FG1.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.FG1.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 541 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 541 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 141
Checking for and removing duplicates
Writing label file ./rh.FG1.mpm.vpnl.label 682
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.FG2.mpm.vpnl.label --trgsubject subjectname --trglabel ./rh.FG2.mpm.vpnl.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.FG2.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.FG2.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 721 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 721 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 151
Checking for and removing duplicates
Writing label file ./rh.FG2.mpm.vpnl.label 872
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.FG3.mpm.vpnl.label --trgsubject subjectname --trglabel ./rh.FG3.mpm.vpnl.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.FG3.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.FG3.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 1523 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 1523 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 139
Checking for and removing duplicates
Writing label file ./rh.FG3.mpm.vpnl.label 1662
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.FG4.mpm.vpnl.label --trgsubject subjectname --trglabel ./rh.FG4.mpm.vpnl.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.FG4.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.FG4.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 1586 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 1586 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 180
Checking for and removing duplicates
Writing label file ./rh.FG4.mpm.vpnl.label 1766
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.hOc1.mpm.vpnl.label --trgsubject subjectname --trglabel ./rh.hOc1.mpm.vpnl.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.hOc1.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.hOc1.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 3667 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 3667 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 652
Checking for and removing duplicates
Writing label file ./rh.hOc1.mpm.vpnl.label 4319
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.hOc2.mpm.vpnl.label --trgsubject subjectname --trglabel ./rh.hOc2.mpm.vpnl.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.hOc2.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.hOc2.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 2719 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 2719 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 810
Checking for and removing duplicates
Writing label file ./rh.hOc2.mpm.vpnl.label 3529
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.hOc3v.mpm.vpnl.label --trgsubject subjectname --trglabel ./rh.hOc3v.mpm.vpnl.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.hOc3v.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.hOc3v.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 1228 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 1228 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 425
Checking for and removing duplicates
Writing label file ./rh.hOc3v.mpm.vpnl.label 1653
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject subjectname --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.hOc4v.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.hOc4v.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 1025 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 1025 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 351
Checking for and removing duplicates
Writing label file ./rh.hOc4v.mpm.vpnl.label 1376
mri_label2label: Done
mris_label2annot --s subjectname --ctab /opt/freesurfer-7.3.2/average/colortable_vpnl.txt --hemi rh --a mpm.vpnl --maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l rh.FG2.mpm.vpnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label --l rh.hOc1.mpm.vpnl.label --l rh.hOc2.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl.label --l rh.hOc4v.mpm.vpnl.label
Reading ctab /opt/freesurfer-7.3.2/average/colortable_vpnl.txt
Number of ctab entries 9
7.3.2
cwd /tmp/tmps594ishs/freesurfer_output/subjectname/label
cmdline mris_label2annot --s subjectname --ctab /opt/freesurfer-7.3.2/average/colortable_vpnl.txt --hemi rh --a mpm.vpnl --maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l rh.FG2.mpm.vpnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label --l rh.hOc1.mpm.vpnl.label --l rh.hOc2.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl.label --l rh.hOc4v.mpm.vpnl.label
sysname Linux
hostname fv-az1121-699
machine x86_64
user runner
subject subjectname
hemi rh
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
ColorTable /opt/freesurfer-7.3.2/average/colortable_vpnl.txt
AnnotName mpm.vpnl
nlables 8
LabelThresh 0 0.000000
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.orig
1 1376057 FG1
2 16711935 FG2
3 16711680 FG3
4 1705837 FG4
5 25600 hOc1
6 255 hOc2
7 16776960 hOc3v
8 65535 hOc4v
Mapping unhit to unknown
Found 114125 unhit vertices
Writing annot to /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.mpm.vpnl.annot
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject subjectname --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA1_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.BA1_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 876 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 876 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 37
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 913
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject subjectname --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA2_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.BA2_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 2688 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 2688 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 23
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 2711
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject subjectname --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA3a_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.BA3a_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 1698 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 1698 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 9
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1707
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject subjectname --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA3b_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.BA3b_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 2183 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 2183 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 38
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2221
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject subjectname --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA4a_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.BA4a_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 1388 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 1388 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 37
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1425
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject subjectname --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA4p_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.BA4p_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 1489 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 1489 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 61
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1550
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject subjectname --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA6_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.BA6_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 6959 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 6959 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 285
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 7244
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject subjectname --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA44_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.BA44_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 1012 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 1012 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 58
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1070
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject subjectname --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.BA45_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.BA45_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 1178 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 1178 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 104
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1282
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject subjectname --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.V1_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.V1_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 3232 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 3232 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 541
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 3773
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject subjectname --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.V2_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.V2_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 3437 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 3437 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 1005
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 4442
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject subjectname --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.MT_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.MT_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 268 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 268 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 19
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 287
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject subjectname --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.entorhinal_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.entorhinal_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 694 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 694 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 11
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 705
mri_label2label: Done
mri_label2label --srcsubject fsaverage --srclabel /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject subjectname --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface
srclabel = /tmp/tmps594ishs/freesurfer_output/fsaverage/label/rh.perirhinal_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = subjectname
trglabel = ./rh.perirhinal_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
FREESURFER_HOME /opt/freesurfer-7.3.2
Loading source label.
Found 291 points in source label.
Starting surface-based mapping
Reading source registration
/tmp/tmps594ishs/freesurfer_output/fsaverage/surf/rh.sphere.reg
Rescaling ... original radius = 100
Reading target surface
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white
Reading target registration
/tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Building source registration hash (res=16).
INFO: found 291 nlabel points
Performing mapping from target back to the source label 128513
Number of reverse mapping hits = 3
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 294
mri_label2label: Done
mris_label2annot --s subjectname --hemi rh --ctab /opt/freesurfer-7.3.2/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.perirhinal_exvivo.label --l rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose
Reading ctab /opt/freesurfer-7.3.2/average/colortable_BA.txt
Number of ctab entries 15
7.3.2
cwd /tmp/tmps594ishs/freesurfer_output/subjectname/label
cmdline mris_label2annot --s subjectname --hemi rh --ctab /opt/freesurfer-7.3.2/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.perirhinal_exvivo.label --l rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose
sysname Linux
hostname fv-az1121-699
machine x86_64
user runner
subject subjectname
hemi rh
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
ColorTable /opt/freesurfer-7.3.2/average/colortable_BA.txt
AnnotName BA_exvivo
nlables 14
LabelThresh 0 0.000000
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.orig
1 1530880 BA1_exvivo
2 16749699 BA2_exvivo
3 16711680 BA3a_exvivo
4 3368703 BA3b_exvivo
5 1376196 BA4a_exvivo
6 13382655 BA4p_exvivo
7 10036737 BA6_exvivo
8 2490521 BA44_exvivo
9 39283 BA45_exvivo
10 3993 V1_exvivo
11 8508928 V2_exvivo
12 10027163 MT_exvivo
13 16422433 perirhinal_exvivo
14 16392598 entorhinal_exvivo
Mapping unhit to unknown
Found 89277 unhit vertices
Writing annot to /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.BA_exvivo.annot
mris_label2annot --s subjectname --hemi rh --ctab /opt/freesurfer-7.3.2/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose
Reading ctab /opt/freesurfer-7.3.2/average/colortable_BA.txt
Number of ctab entries 15
7.3.2
cwd /tmp/tmps594ishs/freesurfer_output/subjectname/label
cmdline mris_label2annot --s subjectname --hemi rh --ctab /opt/freesurfer-7.3.2/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose
sysname Linux
hostname fv-az1121-699
machine x86_64
user runner
subject subjectname
hemi rh
SUBJECTS_DIR /tmp/tmps594ishs/freesurfer_output
ColorTable /opt/freesurfer-7.3.2/average/colortable_BA.txt
AnnotName BA_exvivo.thresh
nlables 14
LabelThresh 0 0.000000
Loading /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.orig
1 1530880 BA1_exvivo
2 16749699 BA2_exvivo
3 16711680 BA3a_exvivo
4 3368703 BA3b_exvivo
5 1376196 BA4a_exvivo
6 13382655 BA4p_exvivo
7 10036737 BA6_exvivo
8 2490521 BA44_exvivo
9 39283 BA45_exvivo
10 3993 V1_exvivo
11 8508928 V2_exvivo
12 10027163 MT_exvivo
13 16422433 perirhinal_exvivo
14 16392598 entorhinal_exvivo
Mapping unhit to unknown
Found 106336 unhit vertices
Writing annot to /tmp/tmps594ishs/freesurfer_output/subjectname/label/rh.BA_exvivo.thresh.annot
mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab subjectname rh white
computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /tmp/tmps594ishs/freesurfer_output/subjectname/mri/wm.mgz...
reading input surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white...
reading input pial surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.pial...
reading input white surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 234693
Total vertex volume 234487 (mask=0)
Saving annotation colortable ./BA_exvivo.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1414190 mm^3 (det: 1.377541 )
968 516 2178 2.769 0.527 0.110 0.018 9 0.7 BA1_exvivo
2816 1759 4904 2.662 0.675 0.071 0.010 10 1.1 BA2_exvivo
1072 746 1193 2.101 0.449 0.106 0.015 6 0.7 BA3a_exvivo
1971 1245 2730 1.950 0.512 0.078 0.010 10 1.0 BA3b_exvivo
1587 844 3275 3.467 0.497 0.070 0.011 6 0.7 BA4a_exvivo
1285 781 2380 3.240 0.578 0.072 0.008 5 0.5 BA4p_exvivo
8187 5059 18079 3.173 0.623 0.100 0.018 53 6.5 BA6_exvivo
3300 2253 6440 2.756 0.675 0.103 0.015 25 2.3 BA44_exvivo
3926 2715 7917 2.575 0.572 0.109 0.018 32 3.1 BA45_exvivo
3468 2538 6129 2.179 0.684 0.126 0.027 34 4.5 V1_exvivo
7975 5577 13424 2.161 0.632 0.140 0.033 93 11.6 V2_exvivo
1851 1278 2979 2.302 0.642 0.113 0.021 15 1.7 MT_exvivo
325 232 544 2.136 0.710 0.113 0.015 2 0.2 perirhinal_exvivo
505 345 1596 3.117 0.905 0.082 0.011 4 0.2 entorhinal_exvivo
mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab subjectname rh white
computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /tmp/tmps594ishs/freesurfer_output/subjectname/mri/wm.mgz...
reading input surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white...
reading input pial surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.pial...
reading input white surface /tmp/tmps594ishs/freesurfer_output/subjectname/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 234693
Total vertex volume 234487 (mask=0)
Saving annotation colortable ./BA_exvivo.thresh.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1414190 mm^3 (det: 1.377541 )
645 345 1452 2.752 0.489 0.112 0.018 6 0.5 BA1_exvivo
1640 998 3250 2.885 0.710 0.055 0.007 4 0.5 BA2_exvivo
960 672 1017 2.106 0.441 0.112 0.015 6 0.7 BA3a_exvivo
1550 1005 1861 1.818 0.418 0.068 0.007 6 0.5 BA3b_exvivo
983 505 1996 3.373 0.591 0.081 0.014 5 0.5 BA4a_exvivo
1111 672 2108 3.383 0.580 0.066 0.008 3 0.4 BA4p_exvivo
5117 3116 11073 3.132 0.625 0.095 0.017 32 3.8 BA6_exvivo
849 594 2184 3.203 0.731 0.108 0.016 7 0.6 BA44_exvivo
1085 780 2372 2.643 0.568 0.135 0.024 12 1.2 BA45_exvivo
3322 2429 5565 2.135 0.646 0.124 0.027 32 4.2 V1_exvivo
4156 2919 7279 2.177 0.738 0.149 0.035 55 6.7 V2_exvivo
234 172 486 2.393 0.727 0.114 0.020 2 0.2 MT_exvivo
26 17 31 2.010 0.348 0.070 0.012 0 0.0 perirhinal_exvivo
499 347 1336 2.866 0.935 0.084 0.009 2 0.2 entorhinal_exvivo
Started at Thu Jun 12 21:05:13 UTC 2025
Ended at Fri Jun 13 02:06:23 UTC 2025
#@#%# recon-all-run-time-hours 5.019
recon-all -s subjectname finished without error at Fri Jun 13 02:06:23 UTC 2025
done
!ls ./freesurfer_output/subjectname/mri
T1.mgz mri_nu_correct.mni.log.bak
antsdn.brain.mgz norm.mgz
aparc+aseg.mgz nu.mgz
aparc.DKTatlas+aseg.mgz orig
aparc.a2009s+aseg.mgz orig.mgz
aseg.auto.mgz orig_nu.mgz
aseg.auto_noCCseg.label_intensities.txt rawavg.mgz
aseg.auto_noCCseg.mgz rh.ribbon.mgz
aseg.mgz ribbon.mgz
aseg.presurf.hypos.mgz segment.dat
aseg.presurf.mgz surface.defects.mgz
brain.finalsurfs.mgz talairach.label_intensities.txt
brain.mgz talairach.log
brainmask.auto.mgz talairach_with_skull.log
brainmask.mgz transforms
ctrl_pts.mgz wm.asegedit.mgz
filled.auto.mgz wm.mgz
filled.mgz wm.seg.mgz
lh.ribbon.mgz wmparc.mgz
mri_nu_correct.mni.log
!ls ./freesurfer_output/subjectname/surf
autodet.gw.stats.lh.dat lh.smoothwm.K1.crv rh.inflated.nofix
autodet.gw.stats.rh.dat lh.smoothwm.K2.crv rh.jacobian_white
lh.area lh.smoothwm.S.crv rh.orig
lh.area.mid lh.smoothwm.nofix rh.orig.nofix
lh.area.pial lh.sphere rh.orig.premesh
lh.avg_curv lh.sphere.reg rh.pial
lh.curv lh.sulc rh.pial.T1
lh.curv.pial lh.thickness rh.qsphere.nofix
lh.defect_borders lh.volume rh.smoothwm
lh.defect_chull lh.w-g.pct.mgh rh.smoothwm.BE.crv
lh.defect_labels lh.white rh.smoothwm.C.crv
lh.defects.pointset lh.white.H rh.smoothwm.FI.crv
lh.fsaverage.sphere.reg lh.white.K rh.smoothwm.H.crv
lh.inflated lh.white.preaparc rh.smoothwm.K.crv
lh.inflated.H lh.white.preaparc.H rh.smoothwm.K1.crv
lh.inflated.K lh.white.preaparc.K rh.smoothwm.K2.crv
lh.inflated.nofix rh.area rh.smoothwm.S.crv
lh.jacobian_white rh.area.mid rh.smoothwm.nofix
lh.orig rh.area.pial rh.sphere
lh.orig.nofix rh.avg_curv rh.sphere.reg
lh.orig.premesh rh.curv rh.sulc
lh.pial rh.curv.pial rh.thickness
lh.pial.T1 rh.defect_borders rh.volume
lh.qsphere.nofix rh.defect_chull rh.w-g.pct.mgh
lh.smoothwm rh.defect_labels rh.white
lh.smoothwm.BE.crv rh.defects.pointset rh.white.H
lh.smoothwm.C.crv rh.fsaverage.sphere.reg rh.white.K
lh.smoothwm.FI.crv rh.inflated rh.white.preaparc
lh.smoothwm.H.crv rh.inflated.H rh.white.preaparc.H
lh.smoothwm.K.crv rh.inflated.K rh.white.preaparc.K
from ipyniivue import NiiVue
nv = NiiVue(crosshair_color=[0,1,0,1])
nv.load_volumes([{"path": "./freesurfer_output/subjectname/mri/orig.mgz"},
{"path": "./freesurfer_output/subjectname/mri/aseg.mgz"}])
nv
from IPython.display import Image
Image(url='https://raw.githubusercontent.com/NeuroDesk/example-notebooks/refs/heads/main/books/images/freesurfer_orig_aseg.png')
